While not revealing which way he will vote in September, the best selling author of the Mma Ramotswe novels and Scotland Street books said that he felt sadness that the "very difficult issue" had split the country.
He told an audience at the Edinburgh International Book Festival that he would not be introducing any referendum themes into his books.
The writer said: "I feel very strongly that I shouldn't in those books espouse any political position.
"There are references to issues which are political in the general sense but I think it would be a bit of a abuse of my situation to use it to expound on my private views.
"I know it's a tricky issue, a very difficult issue for people in Scotland, and I think I would prefer not to bring that into the books.
"I think it's a sad situation that Scotland has become so divided.
"We are now a divided country ...one of my characters in declares himself a 'Scottish patriot but I feel it's very important that it does not affect my affection for our neighbours' and I feel that is very true."
McCall Smith also said he was working on the libretto for a new opera about the Soviet spy Anthony Blunt which should be completed next year.
The two main female characters will be the late Queen Mother and Margaret Thatcher, he said.
"It's really exciting because there is so much to that story," he said.
"You have action, loyalty, betrayal, the sense of horror that you have when you thought you were supporting something you thought was ideologically attractive but is a tyranny, and the fear of discovery."
He also said he had rewritten Jane Austen's Emma, set in modern times in the Norfolk countryside.