By virtue of their high uniformity and stability, metal oxide-based surface-enhanced Raman spectroscopy (SERS) substrates have attracted enormous attention for molecular trace detection. However, strategies for further enhancing the SERS sensitivity are still desired. Herein, MoO_x/WO_x nano-heterojunctions are constructed by mixing MoO_x and WO_x together (MoO_x/WO_x hybrid) with diverse weight ratios. Using a 532 nm laser as the excitation source and R6G as the Raman reporter, it is shown that the Raman signal intensity (for the peak @ 1360 cm^–1) obtained on the optimal MoO_x/WO_x hybrid (MoO_x/WO_x = 1:1/3) is twice that observed on a pure MoO_x or WO_x substrate. Moreover, a limit of detection of 10^–8 M and an enhancement factor of 10⁸ are achieved. In the SERS enhancement mechanism investigation, it is revealed that MoO_x and WO_x form a staggered band structure. During the SERS measurement, electron–hole pairs are generated in the nano-heterojunction using the incident laser. They are then separated by the built-in potential with the electrons moving toward WO_x. The accumulated electrons on WO_x are further transferred to the R6G molecules through the coupling of orbitals. Consequently, the molecular polarizability is amplified, and SERS performance is enhanced. The abovementioned explanation is supported by the evidence that the contribution of the chemical enhancement mechanism in the optimal MoO_x/WO_x hybrid substrate is about 2.5 times or 5.9 times that in the pure WO_x or MoO_x substrate.