In this work, we employ an atomic force microscopy-based technique, Kelvin probe force microscopy, to analyze heterogeneities of four different 2D/3D Ge/MoS2 heterostructures with Ge chemical vapor deposition (CVD) time. High-contrast spatially resolved contact potential difference (CPD) maps reveal the evolution of the samples by Ge deposition. The CPD map in an as-prepared sample does not display any heterogeneity, but CPD contrasts along the grain boundaries are obviously noticed as Ge is deposited on MoS2. With a sufficiently long Ge CVD deposition time, strong grain-to-grain CPD variations over the 2D/3D heterostructures are observed. The results show the variations of the work function from grain to grain that are attributed to the strain induced by the Ge island formation on the cracked MoS2 initiated by sulfur vacancies.