Moffat took over as boss of the hit sci-fi show in 2010, and sanctioned pioneering stories which some fans have complained are complicated and confusing.
However, the writer has shrugged off the criticism, insisting the scripts are suitable as the show is popular around the world.
He tells the BAFTA Guru website, "There's been a weird backlash among, I presume, fairly stupid people about the fact the shows are complicated and clever, but (it is a) huge international hit... We make no apology. Don't expect to do the ironing; sit down, pay attention and think about it.
"Audiences like complexity. They follow intricately plotted soap operas all the time. It depresses me when people say, 'It's all far too clever.'"
Karen Gillan is to come to the end of her tenure as Dr Who's trusty sidekick Amy Pond later this year, when she will be replaced by Jenna-Louise Coleman - story and pictures here.
Do you think the Doctor Who storylines are too complicated? Have your say below...