The author examines the different defect effects of chemical vapor deposition graphene monolayer (CVD‐GM) relying on domain position at an individual nanoparticle‐on‐mirror (NPoM) plasmonic junction. The NPoM, composed of Au nanoparticle (NP)/CVD‐GM/Au thin film (TF), could previously show the mode‐selective Raman enhancement, in which the center domain exhibited the highest Raman enhancement of both radial breathing like mode (RBLM) and D mode considering the local z‐directional electromagnetic (EM) field enhancement effect in the NPoM. Meanwhile, the outer domain of the NPoM also displays the near‐two symmetrical deep pits via atomic force microscope (AFM) with the accompanying lower I[D]/I[D*], higher FWHM[RBLM], I[RBLM], and relatively red‐shifted (tensile strained) Max [RBLM] from surface‐enhanced Raman scattering (SERS) information than the central case. With these observations, the physical loading of Au NP on CVD‐GM/Au TF may induce the threading effect on the most outer position of CVD‐GM at the NPoM, leading to sp2 defect‐rich domains. In contrast, the central domains, where the sp3 defects are rich, exhibit the opposite SERS spectral phenomena, indicating that the near‐flat surface shape of Au NP bottom has a higher probability to exert a strong charge transfer along the z‐direction, resulting in higher I[RBLM] and I[D]/I[D*] than the most outer domain. As such, the author anticipates various chemical sensing using subtle changes in CVD‐GM morphology at both the most outer and center positions in the NPoM with the comparison of each SERS spectral signature.