Disclosed is a manufacturing method of a silicon carbide-based honeycomb structure, which can improve the operating efficiency of a kiln and achieve a long life of fuel bundles. The manufacturing method (1) of the silicon carbide-based honeycomb structure comprises a firing step (S1) in which extruded honeycomb formed bodies (2) containing a silicon carbide-based component are introduced into a firing furnace (4) together with fuel assemblies (3) and the honeycomb formed bodies (2) are fired, thereby producing the silicon carbide based honeycomb structure, wherein the fuel assemblies (3) is formed using a ceramic material containing 70% by weight or more of alumina; the firing step (S1) further comprises an inert gas supply step (S2) in which argon (8) is supplied to a furnace space (5) ofthe firing furnac (4); and a gas addition step (S3) in which methane is introduced as reduction gas (11) to be added to a furnace chamber (5).