Surface Enhanced Raman spectroscopy (SERS) is a molecular-specific analytical technique with various applications. Although electromagnetic (EM) and chemical (CM) mechanisms have been proposed to be the main origins of SERS, exploring highly sensitive SERS substrates with well-defined mechanistic pathways remains challenging. Since surface and electronic structures of substrates were crucial for SERS activity, zero-valent transition metals (Fe and Cu) were intercalated into MoO to modulate its surface and electronic structures, leading to unexceptional high enhancement factors (1.0×10 and 1.1×10 for Fe-MoO and Cu-MoO , respectively) with decent reproducibility and stability. Interestingly, different mechanistic pathways (CM and EM) were proposed for Fe-MoO and Cu-MoO according to mechanistic investigations. The different mechanisms of Fe-MoO and Cu-MoO were rationalized by the electronic structures of the intercalated Fe(0) and Cu(0), which modulates the surface and electronic structures of Fe-MoO and Cu-MoO to differentiate their SERS mechanisms.