Ma was speaking at an Alibaba investor conference hours after Washington said it would impose duties on an extra $200 billion worth of Chinese imports, drawing a warning from Beijing that it would retaliate.
Ma said trade tensions would likely impact Chinese and foreign companies immediately and negatively. He predicted that Chinese businesses would move production to other countries in the medium-term to get around the tariffs.
"You may win the battle, but you lose the war," Ma said at the shareholder event in Hangzhou.
"Middle term, a lot of Chinese business will move to other countries," he added.
Ma said new trade rules were needed over the longterm.
"Even if Donald Trump retired, the new president will come, it will still continue...We need new trade rules, we need to upgrade the WTO," he said, referring to the World Trade Organization.
Ma made the comments in what he said was his last speech to shareholders as chairman of the Chinese internet giant.
He announced last week that he will step down within a year and hand the company reins to chief executive Daniel Zhang.
Ma met with U.S. President Donald Trump last year in a high-profile meeting where he promised to create 1 million U.S. jobs linked to small merchants selling items on Alibaba platforms.
Trade relations have since deteriorated between China and the U.S. in a tit-for-tat escalation in tariffs.