Heavy metal contamination has become a serious and widespread problem in urban environment. Understanding its controlling factors is vital for the identification, prevention, and remediation of pollution sources. This study aimed to identify the factors controlling heavy metal accumulation in urban topsoil using the geodetector method and multiple data sources. Environmental factors including geology, relief (elevation, slope, and aspect), and organism (land-use and vegetation) were extracted from a geological thematic map, digital elevation model, and time-series of Landsat images, respectively. Then, the power of determinant (q) was calculated using geodetector to measure the affinity between the environmental factors and arsenic (As) and lead (Pb). Geology was the dominant factor for As distribution in the this study area; it explained 38% of the spatial variation in As, and nonlinear enhancements were observed for the interactions between geology and elevation (q = 0.50) and slope (q = 0.49). Land-use and vegetation bi-enhanced each other and explained 39% of the spatial variation in Pb. These results indicated that geology and relief were the factors controlling the spatial distribution of As, and organism factors, especially anthropogenic activities, were the factors controlling the spatial distribution of Pb in the study area. As was derived from weathering transportation, and deposition processes of original bedrock and subsequent pedogenesis, and anthropogenic activity was the most likely source of Pb contamination in urban topsoil in Shenzhen. Moreover, geodetector provided evidence to explore the factors controlling spatial patterns of heavy metals in soils.