The multiple Emmy winner received nods in both the comedy and drama categories for the 66th annual prizegiving.
Cranston, who played drug kingpin Walter White on Breaking Bad, was nominated for outstanding directorial achievement in a dramatic series for the episode Blood Money, as well as outstanding directorial achievement in a comedy series for the Modern Family episode The Old Man & The Tree.
Cranston will be up against Breaking Bad creator and executive producer Vince Gilligan for his work on the series finale, Felina, in the drama category, along with David Fincher for House of Cards, Lesli Linka Glatter for Homeland and David Nutter for Game of Thrones.
In the comedy category, the actor will face off against fellow Modern Family director Gail Mancuso, Anthony Rich and Mark Cendrowski for The Big Bang Theory and Beth McCarthy-Miller for 30 Rock's series finale.
McCarthy-Miller nabbed another nomination in the movies for television and miniseries category for her work in The Sound of Music Live!, along with Rob Ashford. They are up against Stephen Frears for Muhammad Ali's Greatest Fight, David Mamet for Phil Spector, Nelson McCormick for Killing Kennedy, and Steven Soderbergh for Behind the Candelabra.
The winners will be announced at the DGA Awards ceremony on 25 January.