The Lib Dem leader said that the fact that the two parties had entered into a coalition together did not mean that they were "joined at the hip".
He acknowledged, however, that he and David Cameron would be defending a "shared record" at the polls and that the debate between them would be "more civilised" than normal.
"We will fight the next general election as separate and independent parties," he told BBC1's The Andrew Marr Show.
"Coalition is not a pact, it is not a merger, it doesn't mean that you become joined at the hip. It means that you retain your separate identities.
"Clearly we will be not only setting out different and separate visions for the future but, yes, we will also be drawing on a shared record of what we sought to achieve during this five-year parliament."
His comments come amid anger among some Tory MPs at what they saw as a "soft-pedalling" by their party in the recent Oldham East and Saddleworth by election campaign in order to prevent a collapse of the Liberal Democrat vote.
Mr Clegg acknowledged that he had suffered "vilification" after abandoning his pledge to oppose any increase in university tuition fees, but insisted that he could cope.
"We went into this with our eyes open. You don't enter go into government at time when you are dealing with this vast, vast black hole, when there's no money left, and think it's going to be a walk in the park," he said.
"You certainly don't join the Government when you are dealing with these very, very big issues and somehow think you are going to be exempt from vilification. Far from it. I've got broad shoulders and a thick skin."
He said that with both Conservatives and Labour committed at the general election to raising tuition fees, the Lib Dems – as the third party – had no choice but to compromise.
"Even if we had gone into coalition with Labour, fees would have gone up. We were completely isolated on this. When it came to negotiating the coalition agreement there was no alternative," he said.
"We were condemned to compromise with other parties."