The Axi low-sulfidation (LS) epithermal deposit in northwestern China is the result of geological controls on hydrothermal fluid flow through strike-slip faults. Such controls occur commonly in LS epithermal deposits worldwide, but unfortunately, these have not been quantitatively analyzed to determine their spatial relationships with gold distribution and further guide mineral prospecting. In this study, we conduct a 3D mineral prospectivity modeling approach for the Axi deposit involving 3D geological modeling, 3D spatial analysis, and prospectivity modeling. The spatial analysis of geometric features revealed the gold mineralization trends in convex segments (0–20 m) with a specific distance from fault 2, the lower interface of late volcanic phase, and the upper interface of phyllic alteration with steep slopes (>65°), implying that gold deposition was significantly controlled by the morphological characteristics and distance fields of geologic features. The present alteration–mineralization zone at Axi has a larger width in bending sites (sections No. 35–15 and No. 40–56) than elsewhere, indicating the location of two fluid conduits extending to depth. The prediction-area plots and receiver operating characteristic curves demonstrated that (genetic algorithm optimized support vector regression (GA-SVR)) outperformed multiple nonlinear regression and fuzzy weights-of-evidence, which was proposed as a robust method to solve complicated nonlinear and high-dimensional issues in prospectivity modeling. Our study manifests spatial controls of structure, host rock, and alteration on LS epithermal gold deposition, and highlights the capability of GA-SVR for identifying deposit-scale potential epithermal gold mineralization.