In comments that will terrify Brussels, Ted Malloch said the EU had become "bloated" by bureaucracy and "anti-Americanism".
And he called for member states to hold their own Brexit-style referendums – which could spark the break-up of the union.
It comes after Mr Trump hailed Brexit as a "blessing to the world" and said the UK would be far stronger outside the bloc.
Mr Malloch, who is the President's pick to become Washington's envoy to Brussels, made the comments in The Parliament magazine.
He said: "Put the EU to a referendum vote in every member country.
"It is time for greater scepticism and realism about the European Union and its not so hidden agenda and ever closer union."
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The European Union has become undemocratic and bloated
He added: "The failure of the European integration project should by now be self-apparent to everyone.
"This is simply not something Churchill or Roosevelt would countenance.
"The European Union has become undemocratic and bloated by both bureaucracy and rampant anti-Americanism."
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Malloch called the EU 'intrinsically undemocratic and unaccountable'
Mr Malloch also called for the US to re-evaluate its view of Brussels.
He said: "We want democracy and accountability, while the EU is intrinsically undemocratic and unaccountable.
"So should the US continue to promote such a damaged European model, which is alien to our own traditions? Is it not working against US interests to do so?"
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