Manning, who was convicted of leaking documents to Wikileaks in 2010, recently had her sentence commuted by former President Barack Obama.
The transgender US Army private, born Bradley Manning, said in an op-ed that Mr Obama's legacy was not bold enough.
Mr Trump took to Twitter to criticise her for calling Mr Obama a weak leader.
The turbulent life of Chelsea Manning
"Ungrateful TRAITOR Chelsea Manning, who should never have been released from prison, is now calling President Obama a weak leader. Terrible!" he tweeted.
His Thursday morning tweet appeared to be referring to Manning's first op-ed in the Guardian newspaper since former President Obama had her sentence reduced last week.
Manning's column suggested Mr Obama had "very few permanent accomplishments" because his attempts at compromise were met with "unparalleled resistance from his opponents, many of whom wanted him to fail".
"The one simple lesson to draw from President Obama's legacy: Do not start off with a compromise," she wrote.
"They won't meet you in the middle. Instead, what we need is an unapologetic progressive leader.
"Our opponents will not support us nor will they stop thwarting the march toward a just system that gives people a fighting chance to live.
"Our lives are at risk - especially for immigrants, Muslim people and black people," she continued.
Mr Trump's choice of words - "ungrateful traitor" and "weak leader" - were also used in a Fox News report on Ms Manning's column aired just minutes before his tweet, reports US media.
Manning was sentenced to 35 years in 2013 for her role in leaking diplomatic cables to the anti-secrecy group.
The leak was one of the largest breaches of classified material in US history.
She is due to be freed from the military prison at Fort Leavenworth, Kansas on 17 May instead of her scheduled 2045 release.
Chelsea Manning is an "ungrateful traitor" who "should never have been released from prison", President Donald Trump has said on Twitter.