"When you start to do bilateral things, it also very much could be used against you," Dimon said in an interview that aired Thursday on "Squawk Box."
"What we're doing in some of these places has now opened the door for much more complicated trade negotiations with our allies," Dimon said. "We should be working with our allies because we have a common interest."
On Tuesday, White House economic advisor Larry Kudlow told Fox that Trump is "very seriously contemplating" separate trade negotiations with Canada and Mexico rather than pursue multilateral reforms to the North American Free Trade Agreement.
Canadian Prime Minister Justin Trudeau subsequently told the Canadian Press that Ottawa will pursue a trilateral deal because it is better for all three countries. The Mexican government did not respond to a CNBC email for comment.
White House press secretary Sarah Huckabee Sanders said Tuesday that the president has not made a decision but is "open to having individual deals."
Regarding the U.S. trade dispute with China, Dimon said the Business Roundtable that he chairs agrees the Trump has "raised some very critical issues" regarding state-owned enterprises, fair competition, market access and foreign ownership of a company in China.
But the "Roundtable has been quite clear we don't think tariffs is the way to do it," Dimon said. He said the U.S. should not work against Beijing but instead set global standards the Chinese eventually will have to adhere to.
Dimon said in a conference call with reporters on Tuesday that the Trump administration's trade policy could become one of the "flies in the ointment" that ends the economic recovery. He maintained in his comments to CNBC that the U.S. economy is in good shape despite uncertainty on trade.
"The president's doing [things] his way. I hope it works," Dimon said. "We're going to try to support it as much as we can. I personally would do some of these things differently."