Mr Trump inherited the official presidential account as he was sworn in as America's 45th president.
The original image showed flag-waving crowds in front of the US Capitol.
But it was changed about an hour later, amid claims from Mr Trump's opponents that crowds at his inauguration were not as large as in 2013.
Trump supporters on social media branded claims Mr Trump was trying to make his inauguration appear better-attended "pathetic" and a "non-story".
The header image has since changed again from a stock picture of an American flag to an image of the new president gazing out of a window.
Mr Trump's @POTUS account has gained millions of followers since its launch, as all 13.6m followers of Barack Obama's account - now archived at @POTUS44 - are in the process of being ported over to the new Trump account.
The new president's first tweet was a link to a Facebook post of the full text of his inauguration address.
His former twitter account still has more than 20m followers.
Speaking ahead of the event, Mr Trump said his inauguration would have "an unbelievable, perhaps record-setting turnout".
But the number of people who turned out to view his midday swearing-in appeared to be smaller than the estimated two million who turned out for Obama.
Images of the National Mall, taken from the top of the Washington Monument, showed sections of the white matting laid down to protect the grass were largely empty.
There will be no official estimate of the crowd's size to settle the issue.
For decades, the US National Park Service provided official crowd estimates for gatherings on the National Mall.
But the agency stopped providing counts after organisers at 1995's Million Man March threatened a lawsuit. They complained that the National Park Service undercounted attendance at the march.
More people turned out to witness Mr Trump and his entourage travelling along Pennsylvania Avenue to the White House on Friday afternoon.