Joe Hill and Gabriel Rodriguez's IDW Publishing series was honoured at the British Fantasy Society's annual prize-giving event.
The series was up against Jeff Lemire's Animal Man, JH Williams III and W Haden Blackman's Batwoman, Mike Carey and Peter Gross's The Unwritten and Robert Kirkman's The Walking Dead.
The Eisner Award-winning title previously took the British Fantasy Award gong in 2009.
The final, seven-issue Locke & Key miniseries Omega will debut in November.
Woody Allen's Midnight in Paris won the 'Screenplay' category, while Jo Walton's novel Among Others and Adam Nevill's The Ritual were named best fantasy and horror novels respectively.
INJ Culbard's SelfMadeHero adaptation of HP Lovecraft's At the Mountains of Madness took home the graphic novel award in 2011.