Messrs. Stone and Manafort played instrumental roles in the president’s political rise, with Mr. Manafort serving as his campaign chairman in 2016 and Mr. Stone acting as a longtime political confidant. Both men were charged as part of former special counsel Robert Mueller’s investigation of Russian interference in the 2016 election. The elder Mr. Kushner served more than two years in prison.

An analysis by Harvard Law professor and former Justice Department official Jack Goldsmith found that 60 of the 65 pardons Mr. Trump granted before Wednesday went to individuals with personal or political connections to the president. Mr. Trump has bypassed the normal Justice Department process for reviewing pardons, frequently hearing appeals for clemency directly from celebrities or other friends, business associates or political allies.

Mr. Trump has also granted pardons to former law-enforcement officials accused of wrongdoing, as well as numerous political figures accused of crime, including campaign-finance violations. On Tuesday, he pardoned 15 others, among them three former Republican congressmen and several former military contractors convicted of wartime killing of Iraqi civilians.

Mr. Manafort was convicted by a Virginia jury in August 2018 of not paying taxes on more than $16 million in income he earned advising Russia-aligned politicians in Ukraine in the early 2010s, and of lying to two banks from which he sought loans in 2015.

Mr. Manafort also pleaded guilty in Washington to conspiracy. He was sentenced in 2019 to 7½ years in prison.

A presidential pardon won’t end all the legal woes of Mr. Manafort, who is still engaged in a protracted court battle over mortgage fraud and other charges brought in New York state.

“This action underscores the urgent need to hold Mr. Manafort accountable for his crimes against the people of New York as alleged in our indictment," Manhattan District Attorney Cyrus Vance Jr. said.

White House press secretary Kayleigh McEnany said Mr. Manafort “endured years of unfair treatment." Mr. Manafort tweeted: “Mr. President, my family & I humbly thank you."

As part of his plea agreement, Mr. Manafort had agreed to forfeit three New York properties worth more than $10 million and funds held in three bank accounts and a life-insurance policy. The pardon would wipe out that requirement, effectively forcing the government to write Mr. Manafort a check for the millions of dollars in seized assets.

Mr. Manafort was released from federal prison in May because of coronavirus concerns. He had served two years and was set to spend the rest of his sentence in his Virginia home.

While the Mueller investigation was still under way, the president praised Mr. Manafort for having “refused to ‘break’—make up stories in order to get a ‘deal,’" contrasting him favorably to Michael Cohen, Mr. Trump’s former lawyer who cooperated against him in a separate investigation.

The president pardoned Mr. Stone, a longtime friend and political adviser, after commuting his sentence in July, days before Mr. Stone was to report to prison.

He was convicted in federal court last year of making false statements, witness tampering and trying to impede a congressional investigation into Russian election interference, and was sentenced to 40 months in prison.

Ms. McEnany said pardoning Mr. Stone “will help to right the injustices he faced at the hands of the Mueller investigation."

Mr. Kushner, the father of senior White House adviser Jared Kushner, pleaded guilty in 2004 to tax evasion, witness tampering and making illegal campaign donations in a case prosecuted by former New Jersey Gov. Chris Christie. He was sentenced to two years in prison and served 14 months.

The elder Mr. Kushner was accused of hiring a prostitute to seduce his brother-in-law, videotaping their encounter and sending it to his sister, who was being pushed to testify in a criminal investigation of the family business. Mr. Christie called it “one of the most loathsome, disgusting crimes" he had prosecuted.

Ms. McEnany said the elder Mr. Kushner, since finishing his sentence, had “been devoted to important philanthropic organizations and causes."

In 2018, Mr. Kushner told the New York Times, “I would prefer not to have a pardon," saying it would lead to more publicity.

“In pardoning Paul Manafort, Roger Stone and Charles Kushner, President Trump has made it clear that he believes the purpose of the pardon is to bail out rich white men connected to him," said Noah Bookbinder, executive director of the liberal advocacy group Citizens for Responsibility and Ethics in Washington. “Trump has turned an instrument of mercy and justice into just another way for him to be corrupt."

In response to Mr. Trump’s pardons of his associates, Sen. Ben Sasse (R., Neb.) said in a statement: “This is rotten to the core."

Other pardon recipients Wednesday included John Tate and Jesse Benton, Republican consultants to former presidential candidate Ron Paul who were convicted of 2012 campaign-finance violations. Ms. McEnany said their pardons were supported by Sen. Rand Paul, Ron Paul’s son, and by former Federal Election Commission Chairman Lee Goodman, who said the law the two men violated “was unclear and not well established at the time."

Mr. Trump also pardoned former Rep. Mark Siljander, who was sentenced in 2012 to one year in prison for obstructing justice and acting as an unregistered foreign agent for an Islamic charity suspected of ties to terrorism.

Mr. Trump commuted the sentences of three individuals, including two men who founded a real-estate company using a straw CEO and lost millions of investors’ money during the 2008 financial crisis.

Two of the pardons the president granted on Wednesday were supported by Pam Bondi, the former Florida attorney general who defended the president during his Senate impeachment trial, according to the White House. Ms. Bondi supported three of the commutations the president issued a day earlier. The president also granted pardons to individuals supported by other friends and donors, including Newsmax CEO Chris Ruddy and billionaire Ike Perlmutter.

Mr. Trump also has granted pardons to a number of former law-enforcement and immigration officials accused of wrongdoing in the line of duty. His actions announced Wednesday include granting clemency to Stephanie Mohr, a police officer sentenced to prison for misuse of a K-9 dog against a suspect; a pardon of Joseph Occhipinti, a former Immigration and Naturalization Service official charged with lying and deprivation of rights; and Gary Brugman, a former border patrol officer charged in an excessive force case. Earlier in the week, he pardoned two other border patrol officials accused of misuse of force in a border shooting.

Past presidents have also made controversial pardon choices, often right before leaving office. Then-President Clinton pardoned fugitive commodities trader Marc Rich, whose ex-wife was a major donor to the Democratic Party and Mr. Clinton’s presidential library, on his last day in office. President Obama commuted the sentence of Chelsea Manning, convicted on charges related to passing classified documents to WikiLeaks, just days before leaving the White House.

Mr. Trump has discussed with advisers the prospect of pardoning several other associates, as well as members of his family and his personal attorney, Rudy Giuliani, even in the absence of existing criminal charges.