David Macdonald was first on the new pro-Remain party’s list of hopefuls to become an MEP for Scotland when the elections are held on 23 May.
Chuka Umunna, an MP and spokesman for Change UK, said Mr Macdonald had “let down his fellow candidates and activists” by making the “disappointing” decision.
“We are focusing all our efforts on adding to the Remain vote in the UK and challenging the pro-Brexit Tory, Brexit and Labour parties,” he added.
Mr Macdonald told Sky News that he took the decision because “clearly the numbers don’t stack up” for the party.
He said: “It’s been a difficult decision for me, for sure. But certainly one that I’m at peace with.
“I looked at the electoral landscape in Scotland, it’s very very different to that in the rest of the UK.
“We have a very diluted Remain vote in Scotland and it’s becoming clear to me that as we approach these elections, with just over a week to go, that quite clearly the numbers don’t stack up for Change UK. I would hate to see that split the Remain vote in Scotland.
“And for that reason I have decided to publicly support the Scottish Liberal Democrats in the hope that the Change UK supporters that have been supporting us thus far will be reasonable in seeing what we could potentially do here and offer their support to the Scottish Liberal Democrats as well.”
He rejected suggestions from Mr Umunna that he had “let down” those in Change UK.
“I would beg to differ,” Mr Macdonald said.
“I believe the cause overall is the larger combined effort by all the Remain parties to remain in the European Union and to stop Brexit.
“It’s quite clear and apparent to me that the Scottish Liberal Democrats and Change UK in Scotland are singing from almost exactly the same hymn sheet and it’s important that we see the bigger picture here.”
Mr Macdonald was bumped up to the top of the Scottish candidates list when the post was vacated by another candidate who stood down.
The European Parliament elections are on track to go ahead after Britain did not leave the European Union on 29 March.
Tory Brexiteers and the government’s confidence and supply partners, the DUP, united with Labour to reject a divorce deal three times.
Mrs May has repeatedly said she does not want the UK to be holding the elections for a new cohort of 73 MEPs, but it is obliged to while still a member of the EU.
The parties standing in Scotland are Change UK, Conservative, Green, Labour, Liberal Democrats, SNP, Brexit Party, UKIP and independents.