The sides meet at Stamford Bridge for what is a rematch of last season's UEFA Europa League semi-final.
While the Premier League side won through 5-2 on aggregate in that last-four tie, Mourinho is not taking anything for granted this time around, both in terms of the match itself and Chelsea's overall chances in the competition.
"I want us to start this new phase by winning," he said.
"Maybe lots of people think Basel is a team that are not so difficult. I just remember two years ago – Man United out and Basel through – and last year – Tottenham out and Basel through – so it’s a difficult team.
"I want to qualify for that next phase. It's very important for everybody at the club."
Chelsea went on to win the Europa League last season under Rafael Benitez, having triumphed in the Champions League during the previous campaign.
Mourinho has warned his side not to risk dropping into Europe's second-tier competition again this season, but dismissed the idea that he is obsessed with winning the Champions League with Chelsea.
"Last season Chelsea went out of its natural habitat, which is the Champions League. We don’t want to do that again," said Mourinho, who has previously guided Porto and Inter to Champions League titles.
"We don’t want to play in the Europa League, we want to play in the Champions League, and I think when you start the group with a victory it’s a big step towards qualifying.
"In the evolution of this club, it’s very important for these players to play at the highest level and that’s the Champions League, not the Europa League.
"There are no obsessions in football. I never had (an obsession) and I don’t have. I don’t like my team to have (an obsession).
"One thing is an objective and the other is obsession. The first objective of this team is a process we have to go through.
"No obsession for me. No obsession for Chelsea. But I want to win it for a third time and Chelsea want to win for a second time."
Mourinho confirmed that both Frank Lampard and Oscar will start Wednesday's game.
