The Walking Dead and Thief of Thieves are two of the publisher's most popular titles, both of which have inspired television shows.
Stephenson pointed out that the influence of television has been beneficial to these titles, but expressed fears that the industry could suffer as a whole if this trend continues.
"There are way worse problems to have, obviously, and I'm not complaining, but it is a little disconcerting that the dividing line between The Walking Dead and Thief of Thieves and Invincible and Super Dinosaur is the attention the former two titles have received from Hollywood," he wrote on his blog.
"Is that a good thing for those books? Absolutely. But it's a bad thing for comics as a whole, when we sit back and let mainstream popularity guide how we as an industry order and sell comics and how we as a community buy and collect comics.
He added: "In essence, we wait for someone outside comics to tell us something is worthwhile before accepting it ourselves. And that's just plain backwards."
The third season of AMC's The Walking Dead will debut in the autumn. Thief of Thieves is currently in development at the network.