The Scottish Affairs Committee said the impact would be "far greater than acknowledged by the Scottish Government" and called on Holyrood to publish a Plan B.
Ian Davidson MP, chairman of the Scottish Affairs Committee, said: "The Scottish Government has a clear responsibility to tell the Scottish people how it would manage the damaging effects of changes in higher education and research that separation would bring."
The House of Commons report also found that Scottish universities currently receive over 50% more in research grants from the UK Research Councils than they would if allocation of funding was based on population share.
David Willetts, the UK Minister for Universities and Science, told the committee that in the event of separation, "the rest of the UK would carry on with its research councils, Scotland would not be part of that structure".
Holyrood Education Secretary Michael Russell said of the warning: "This committee is mainly made up of anti-independence Tory, LibDem and Labour MPs.
"It is little surprise their report opposes independence.
"With independence, it will be in Scotland's and the UK's interests to maintain a common research area including shared research councils.
"We would negotiate a fair funding formula with Westminster for the future."
A spokesman for the pro-independence group Academics for Yes, said: "The biggest threat to Scotland's higher education and research sector comes from further Westminster cuts in 2015."