Academics at the University of Sussex have suggested a trade arrangement would likely require changes to UK domestic legislation in areas such as drug pricing and food regulation.
They also say it could create a "legal and policy vacuum" regarding the relationship between the UK's devolved nations and the extent to which they can influence UK trade negotiations.
Among the recommendations made by the group is a call to give the devolved nations a formal role in the setting of UK negotiating objects to ensure external trade arrangements do not lead to any internal trade barriers.
Replicating the EU's balance between devolution and harmonisation, with respect to UK-specific rules and bodies, is also put forward, along with a suggestion the UK Government introduces increased legislative assurances that it will not weaken current levels of protection.
"The UK Government may be forced to choose between facilitating trade with the US or holding on to the UK's fragile national identity.
"The destruction of the UK internal market - and potentially the union itself - seems too high a price to pay for a US free trade agreement."
The SNP's Ian Blackford said: "This is a stark warning that the Tories are likely to impose a trade deal on Scotland. We can't allow our NHS to be part of a trade deal with Donald Trump.
"Scotland needs to escape Brexit and lock Boris Johnson out of Downing Street - and only the SNP can beat the Tories in Scotland."