The cartoonist received the Literary Award for 'Outstanding Body of Work in Graphic Lit' for his body of work, which includes Ghost World, Wilson, David Boring and Like a Velvet Glove Cast in Iron.
Clowes has also worked in screenwriting, receiving an Academy Award nomination in 2002 for his adaptation of Ghost World.
Matt Fraction (Fear Itself, Cassanova) was the recipient of the graphic literature award last year, which was the first time that category was featured.
The Pen Centre is a non-profit organisation that aims to "protect the rights of writers around the world [and] to stimulate interest in the written word".
Clowes's Wilson is being adapted into a feature film by Fox Searchlight.
Sideways director Alexander Payne in reportedly in the running to direct the movie.