Surface-enhanced Raman scattering (SERS) is a non-destructive spectra analysis technique. It has the virtues of high detectivity and sensitivity, and has been extensively studied for low-trace molecule detection. Presently, a non-noble-metal-based SERS substrate with excellent enhancement capabilities and environmental stability is available for performing advanced biomolecule detection. Herein, a type of molybdenum carbide/molybdenum oxide (Mo2C@MoOx) heterostructure is constructed, and attractive SERS performance is achieved through the promotion of the charge transfer. Experimentally, Mo2C was first prepared by calcinating the ammonium molybdate tetrahydrate and gelatin mixture in an argon atmosphere. Then, the obtained Mo2C was further annealed in the air to obtain the Mo2C@MoOx heterostructure. The SERS performance was evaluated by using a 532 nm laser as an excitation source and a rhodamine 6G (R6G) molecule as the Raman reporter. This process demonstrates that attractive SERS performance with a Raman enhancement factor (EF) of 1.445 × 108 (R6G@10−8 M) and a limit of detection of 10−8 M can be achieved. Furthermore, the mechanism of SERS performance improvement with the Mo2C@MoOx is also investigated. HRTEM detection and XPS spectra reveal that part of the Mo2C is oxidized into MoOx during the air-annealing process, and generates metal–semiconductor mixing energy bands in the heterojunction. Under the Raman laser irradiation, considerable hole–electron pairs are generated in the heterojunction, and then the hot electrons move towards MoOx and subsequently transfer to the molecules, which ultimately boosts the Raman signal intensity.