Iran is a key energy supplier for Turkey, which is almost 100-percent dependent on fuel imports, with natural gas accounting for nearly 40 percent of the country's electricity production.
"We need to be realistic. Am I supposed to let people freeze in winter? Nobody should be offended. How can I heat my people's homes if we stop purchasing Iran's natural gas?" Reuters quoted Erdogan as saying.
The remarks came just after Trump dedicated a major part of his 30-minute speech to the UN General Assembly in New York to Iran-bashing.
His hardline national security adviser John Bolton pledged that the US would be 'aggressive and unwavering' in enforcing economic sanctions on Iran and not allow the European Union or anyone else to undermine them.
In his address to the United Nations on Tuesday, Erdoğan took a swipe at the United States for using economic sanctions 'as weapons'.
"None of us can remain silent to the arbitrary cancelation of commercial agreements, the spreading prevalence of protectionism and the use of economic sanctions as weapons," he told the UN General Assembly.
Trump's announcement of sanctions and steep new tariffs on Turkish steel and aluminum in August has sent ties between the two allies into a tailspin.
Erdoğan has said "America behaves like wild wolves" and accused the West of waging an economic war on his country which has seen the Turkish lira lose about 40 percent this year alone.
On Tuesday, the Turkish president hit out at "countries that are persistently trying to create chaos", without directly naming the United States. "Nobody wants the world to experience a new economic rupture," he said.
Iran is Turkey's second-biggest supplier of natural gas after Russia and sells about 10 billion cubic meters a year of gas under a 25-year supply deal to Turkey which it uses for electricity generation.
Earlier this month, Erdoğan and his Iranian counterpart Hassan Rouhani called for promoting business ties between the two neighbors in a bid to counter unilateral US sanctions on Tehran and Ankara.
Iran and Turkey opened their first letter of credit in April for business transactions in their national currencies.
Last August, Turkey's Unit International signed a drilling deal worth $7 billion with Russia's state-owned Zarubezhneft and Iran's Ghadir Investment Holding for developing Iranian oil and gas fields.
The agreement marked a new dawn in cooperation between Iranian, Russian and Turkish companies, reflecting on the rapidly changing geopolitical dynamics in the region.