Gen Jones is a former Marine Corps general who served all over the world National Security Adviser Gen James Jones is stepping down and will be replaced by his deputy, Tom Donilon.
President Barack Obama is to announce the high-level staff changes at the White House on Friday, officials said.
Gen Jones’s announcement had been widely expected as Mr Obama nears two years in the White House.
It follows news of the departure of several other senior White House advisers, including political staff and top economic adviser Larry Summers.
Gen Jones, a former Marine Corps general, is the first high-level member of Mr Obama’s national security team to depart.
In recent weeks, Mr Obama’s chief of staff Rahm Emanuel left to run for mayor of Chicago and senior political adviser David Axelrod departed to begin planning the president’s 2012 re-election bid.
As a 2m-tall, crop-headed military veteran with 40 years’ service in the Marine Corps, Gen James Jones had little in common with the slick political professionals who got Mr Obama to the White House. A recent book quoted his descriptions of them as “the water bugs”, “the mafia” and “the campaign set”.
That may have speeded up his departure, but it was widely known that Gen Jones was preparing to leave his job.
His importance to the White House team may have been limited by the closeness to the president of cabinet ministers like Robert Gates and Hillary Clinton and by the direct line that General David Petraeus can command from Afghanistan.
Nonetheless, this is the latest in a string of high-profile departures including budget director Peter Orszag and White House chief of staff Rahm Emanuel. Some turnover is to be expected two years into the gruelling grind of a presidential term, but if the exodus continues it may create the impression of a team that is growing weaker.
Mr Summers, Mr Obama’s top economic adviser, announced last month he would leave at the end of the year to return to Harvard University.
Staff departures are not unusual at this point in a president’s term, nearly halfway through the four years.
Gen Jones is seen as close to the president, while Mr Donilon, a veteran Democratic political hand and former chief of staff to Bill Clinton’s Secretary of State Warren Christopher, is not seen as part of Mr Obama’s inner circle, analysts say.
A recent book by veteran reporter Bob Woodward of the Washington Post quoted Defence Secretary Robert Gates as saying Mr Donilon would be “a disaster” as a national security adviser.
Gen Jones retired from the Marine Corps in 2007 after more than 40 years, taking a position as the State Department’s Special Envoy for Middle East Regional Security.
He was commissioned as a Marine Corps officer in 1967, and was sent to Vietnam. He later served in command and staff positions all over the world.
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