2D transition metal dichalcogenide (TMD) materials have been recognized as active platforms for surface‐enhanced Raman spectroscopy (SERS). Here, the effect of crystal structure (phase) transition is shown, which leads to altered electronic structures of TMD materials, on the Raman enhancement. Using thermally evaporated copper phthalocyanine, solution soaked rhodamine 6G, and crystal violet as typical probe molecules, it is found that a phase transition from 2H‐ to 1T‐phase can significantly increase the Raman enhancement effect on MoX2 (X = S, Se) monolayers through a predominantly chemical mechanism. First‐principle density functional theory calculations indicate that the significant enhancement of the Raman signals on metallic 1T‐MoX2 can be attributed to the facilitated electron transfer from the Fermi energy level of metallic 1T‐MoX2 to the highest occupied molecular orbital level of the probe molecules, which is more efficient than the process from the top of valence band of semiconducting 2H‐MoX2. This study not only reveals the origin of the Raman enhancement and identifies 1T‐MoSe2 and 1T‐MoS2 as potential Raman enhancement substrates, but also paves the way for designing new 2D SERS substrates via phase‐transition engineering.