Tariffs on $156bn of Chinese goods will be imposed if a trade deal is not finalised by December, Steve Mnuchin says.
Steven Mnuchin said he still hoped a tentative US-China deal agreed last week to suspend fresh tariffs would be formally approved.
But his caution, during a CNBC interview, seemed in contrast with President Trump's optimism last week.
Wall Street shares dipped at the open on worries about reaching a final deal.
Last Friday, the US agreed to hold off on a planned 25%-30% tariff increase on Chinese imports that was due to come into effect on Tuesday. It followed two days of talks in Washington between Liu He, China's vice-premier, and US officials.
President Donald Trump, who described the talks as a "love fest", said the preliminary deal would take about five weeks to complete.
He added that he might sign the deal alongside Chinese President Xi Jinping at a United Nations summit in Chile in December.
However, Chinese officials have been more cautious about the outcome, simply claiming there had been progress between the countries.
US officials also warned last week that tariffs on a different set of Chinese goods, which are due to go into effect in December, remained an option.
Mr Mnuchin told CNBC: "I have every expectation if there's not a deal, those tariffs would go in place - but I expect we'll have a deal."
There are still major issues to be negotiated, including industrial subsidies and cybertheft.
Mr Mnuchin said more trade negotiations at various levels would take place over the coming weeks, including a phone call between himself, US Trade Representative Lighthizer, and Mr Liu.
Despite the treasury secretary's caution, analysts said it still look as if talks were progressing. "Investors are trying to wrap their head around this 'non deal'," said Robert Pavlik, chief investment strategist at SlateStone Wealth, in New York.
"If (the market) was really sceptical, it would be selling off a lot harder. But it's not because there are some good points to it - that they are still talking and potentially reaching a deal."
Asked on CNBC about a dispute between China and the US National Basketball Association, stemming from a tweet by Houston Rockets manager Daryl Morey expressing support for pro-democracy protests in Hong Kong, Mr Mnuchin said he hoped the two sides could come to a solution. BBC