Mr Moore claimed the SNP and UKIP had similar arguments as he claimed that both parties had a “hard need to assert a specific sense of national identity”.
The cabinet minister launched the attack on the SNP at a fringe meeting on the issue of Europe at the Lib Dem conference in Glasgow.
The claims come a day after Lib Dem leader Willie Rennie accused the SNP of playing a “dangerous game” as he claimed the party promoted the idea that Scottish identity was the same as support for independence.
Mr Moore went on to claim “nationhood rather than economics” is at the heart of Scottish nationalism as he drew the comparison with the SNP and UKIP.
He insisted that UKIP had its “own high-pitched case” of anti-EU nationalism that has no focus on jobs and the economy.
Mr Moore said: “There is of course a clear parallel between those who want Scotland to leave the UK, and those who want the UK to leave the EU.
“For both the nationalists and the Eurosceptics, there is a hard need to assert a specific sense of national identity.
“That need overrides facts.
“The First Minister has said that nationhood rather than economics is at the heart of Scottish nationalism.
“And Eurosceptics place sovereignty rather than jobs, trade or family finances at the centre of their own high-pitched case.”
The minister went on to claim that the the Lib Dem arguments in favour of Scotland’s place in the UK and Britain’s EU membership are “highly rational and very similar”.
Mr Moore said the SNP and UKIP, which is led by Nigel Farage, “pull in tandem” as he claimed nationalists and Eurosceptics were similar political movements.
He said: “Both families were formed out of a growing sense of cross-border identity, and the realisation that cross-border cooperation benefits us all.
“Whether we talk about the need for a free market, movement of people, or big and specific challenges like climate change, the answer is in partnership not separation.
“For all the noise that these two groups make, and for all they would claim to be in opposition, nationalists and Eurosceptics pull in tandem.
“And stretch to breaking point our national interest.”
Mr Moore claims were dismissed as “absurd” by an SNP spokesman, who said the Lib Dems were in “grave danger of sliding into electoral oblivion” in Scotland.
An SNP spokesman said: “The Lib Dems’ disastrous conference just got worse with this absurd statement by Mr Moore. It is the Tory-led government he is helping to prop up that is dancing to UKIP’s tune at Westminster - which is utterly unrepresentative of Scotland, where UKIP have never once even saved their deposit in an election - and his own party are now pandering to UKIP by moving towards backing a referendum to exit the EU.
“By lurching onto UKIP’s territory and joining other Westminster parties in seeking a referendum on EU membership – which is the only threat to Scotland’s future in Europe –the Lib Dems have more in common with UKIP than they might like to think.
“Indeed, much like UKIP, the latest poll putting Lib Dem support at just 4% in Scotland means they are in grave danger of sliding into electoral oblivion.”
LIBERAL DEMOCRAT CONFERENCE IN GLASGOW