Trump in an executive order on Friday suspended refugees from entering the US and barred visas for travellers from Iran, Iraq, Libya, Somalia, Sudan, Syria and Yemen for the next three months to "keep radical Islamic terrorists out."
His controversial decision has led to chaos at home and around the world, with hundreds of thousands of people gathered at airports across the US in protest against the ban.
The 46-year-old first Muslim mayor of London pointed out that many British citizens will be affected by the new rules and was pleased that UK Prime Minister Theresa May had also raised concerns.
"The USA has a proud history of welcoming and resettling refugees. The President can't just turn his back on this global crisis - all countries need to play their part," he said.
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"I'm pleased that the Prime Minister has now said she and the government do not agree with President Trump's policy, which will affect many British citizens who have dual nationality, including Londoners born in countries affected by the ban," he added.
Khan, the son of a Pakistani bus driver, and the US President have a history of clashing and in the past the Mayor criticised many of Trump's campaign tactics.