Bolton, who as an NSA was a strong supporter of India's anti-terrorism efforts, was in office for only about a year and a half and is Trump's third advisor in his tenure so far of less than three years.
Trump, who often makes important staff announcements on Twitter, tweeted: "I informed John Bolton last night that his services are no longer needed at the White House. I disagreed strongly with many of his suggestions, as did others in the Administration, and therefore I asked John for his resignation, which was given to me this morning."
While during his tenure as US permanent representative to the United Nations in 2005-6, Bolton was highly critical of India, but as NSA, he emerged as a strong supporter of India.
Driven by his strong opposition to terrorism, he backed India during the Pulwama crisis when Pakistan-backed killed about 40 Indian security personnel in Kashmir in February.
Bolton's extremely hardline positions on Afghanistan, North Korea and Iran were often at odds publicly with Trump's diplomatic efforts, sending mixed messages that undermined his efforts.
Trump once said that if Bolton had his way, the US would be in several wars.
He suffered a big setback when Trump cancelled a bombing campaign against Iran in June, that could have led to war.
Trump has expressed interest in meeting personally with Iranian President Hassan Rouhani, while Bolton advocated military confrontation.
Bolton has also opposed Trump's continuing overtures to Kim Jong Un.
Bolton's appointment was a sop to the militant right-wing of Trump's supporters, while running against Trump's campaign promise to pull back from international entanglements and withdraw from Afghanistan.
He reportedly was against attempts by the administration to reach a peace agreement with the Taliban to facilitate US troops withdrawal. That diplomacy crashed when Trump cancelled meeting with the Taliban and Afghan leaders after a Taliban attack killed a US soldier in Afghanistan.
Bolton succeeded Lt. Gen. Michael Flynn, who quit after only 24 days, and Lt. Gen. H. R. MacMaster, who was virtually fired because of policy differences.
Despite his hawkish image, he appeared to have gotten along with US Secretary-General Antonio Gutteres. His spokesperson Stephane Dujarric told reporters that Bolton has had interactions with Guterres in several capacities. Their meetings were cordial, he added.
(Arul Louis can be contacted at arul.l@.in and followed on Twitter @arulouis)
( With inputs from IANS )