Speaking to LBC, he said that, without the deal, the two countries could "do many times the numbers" than now, the BBC reported on Thursday.
The US President also took a swipe at Labour leader Jeremy Corbyn, saying he would be "so bad" as prime minister.
Corbyn accused him of "trying to interfere" in the UK general election to boost "his friend Boris Johnson".
The UK is officially going to the polls on December 12 after the early election bill became law when it was given royal assent on Thursday.
It follows a further delay to the UK's departure from the EU, to January 31, 2020.
In August, Trump promised a "very big trade deal" with the UK and predicted that leaving the EU would be like losing "an anchor round the ankle".
But speaking to friend and supporter Nigel Farage on LBC, Trump was critical of the withdrawal agreement Mr Johnson recently reached with EU leaders.
Trump told LBC: "We want to do trade with UK and they want to do trade with us.
"To be honest with you... this deal... under certain aspects of the (Brexit) deal... you can't do it, you can't do it, you can't trade.
"We can't make a trade deal with the UK because I think we can do many times the numbers that we're doing right now and certainly much bigger numbers than you are doing under the European Union."
The prime minister aims to get his deal through Parliament if he wins the general election.
However, Trump also praised Johnson as "the exact right guy for the times".
In response, a Downing Street spokesman said Johnson's Brexit deal with the EU "ensures that we take back control of our laws, trade, borders and money".
"Under this new deal, the whole of the UK will leave the EU customs union, which means we can strike our own free trade deals around the world from which every part of the UK will benefit."
( With inputs from IANS )