Gold-mediated exfoliation of MoS2 has recently attracted considerable interest. The strong interaction between MoS2 and Au facilitates preferential production of centimeter-sized monolayer MoS2 with near-unity yield and provides a heterostructure system noteworthy from a fundamental standpoint. However, little is known about the detailed nature of the MoS2–Au interaction and its evolution with the MoS2 thickness. Here, we identify the specific vibrational and binding energy fingerprints of this interaction using Raman and X-ray photoelectron spectroscopy, which indicate substantial strain and charge doping in monolayer MoS2. Tip-enhanced Raman spectroscopy reveals heterogeneity of the MoS2–Au interaction at the nanoscale, reflecting the spatial nonconformity between the two materials. Micro-Raman spectroscopy shows that this interaction is strongly affected by the roughness and cleanliness of the underlying Au. Our results elucidate the nature of the MoS2–Au interaction and guide strain and charge doping engineering of MoS2.