In urban areas, variations in the functional usage of buildings or their clusters directly influence the 2D/3D morphology of buildings which can lead to changes in the ventilation potential (VP) at different heights, but there is a lack of refined quantitative relationship analysis between 3D building form parameters (BFPs) and VP at different heights within a certain urban area. The objective of our study is to obtain simulated wind field data from different heights, considering distances from roads, and transverse and longitudinal sections. We employ partial correlation analysis, simple correlation analysis, and Geographic detectors to uncover the extent and mechanisms of the influence of BFPs on the ventilation effectiveness of neighborhoods in a major urban center in China, specifically Nanjing. The findings demonstrate that, at all heights, there is an inverse relationship between wind speed and building density (BD), with the location of higher wind speed generally aligning with the intersection points. The correlation coefficients between BD and simulated wind speed are 0.040 (1.5 m), −0.475 (10 m), and −0.314 (30 m), while the correlation coefficients between building height (BH) and simulated wind speed are 0.237. However, no significant correlation is observed between floor area ratio (FAR) and simulated wind speed. Geographic detector analysis reveals differences in the correlation between BFPs and simulated wind speed at different heights within various building functional areas. Our study provides some practical information for urban planners and designers to carry out wind sensitivity and adaptation planning and urban design.