Three-dimensional (3D) prospectivity modeling based on the weights of evidence and fuzzy logic methods was carried out for the Honghai volcanogenic massive sulfide Cu–Zn deposit in eastern Tianshan, northwestern China. A 3D geological model was constructed using geological maps, geological plans, cross sections, and boreholes. The geological model and metallogenic model of the Honghai deposit were used to generate 3D predictor maps. The weights of evidence method and fuzzy logic were then used to integrate the various predictor maps to create prospectivity maps. Capture efficiency curves were subsequently used to delineate high-prospectivity areas in the prospectivity maps. The weights of evidence method and fuzzy logic delineated 96.13% and 90.60%, respectively, of the known mineralization in the high-prospectivity areas, which occupied about 5.89% and 6.33% of the study area. Receiver operating characteristic (ROC) curves were used to evaluate the performance of the two methods, with both showing area under the curve values > 0.5, which indicates the effectiveness of both methods for 3D prospectivity modeling of the Honghai deposit. However, the weights of evidence method generally performed better than fuzzy logic for identification of the concealed and deep-seated Honghai deposit. Conversely, fuzzy logic exhibited better generalization capability. Based on the findings of this study, the high-prospectivity areas located in the south of the known orebody of the Honghai deposit should be considered as high-priority targets for future mineral exploration. This study aims to enable more effective delineation of concealed and deep-seated exploration targets in the Honghai deposit.