As a developed economic region in China, the problem of heavy metals (HMs) pollution in the Yangtze River Delta has become increasingly prominent. As an important evergreen broad-leaved tree species in southern China, the camphor tree cannot only be used as a street tree but also its various tissues and organs can be used as raw materials for Chinese herbal medicine. In order to explore whether heavy metal contamination in the region threatens the safety of camphor trees as pharmaceutical raw materials, we collected the bark and leaves of the tree most commonly used for pharmaceuticals in Yixing City. Based on the determination of HMs content, the health risks after human intake are evaluated, the sources and contributions of HMs are analyzed, and then the health risks of pollution sources are spatially visualized. The results showed that under the influence of human activities, the camphor trees in the study area had obvious enrichment of HMs, and the over-standard rate of Pb in the bark was as high as 90%. The non-carcinogenic risks of bark and leaves are acceptable, but the carcinogenic risks are not acceptable. The bark had the highest average carcinogenic risk, approaching six times the threshold. The results of Pb isotope ratio analysis showed that the average contribution rate of industrial activities to HMs in camphor trees in the study area was the highest, reaching 49.70%, followed by fossil fuel burning (37.14%) and the contribution of natural sources was the smallest, only 13.16%. The locations of the high-risk areas caused by the three pollution sources in the study area are basically similar, mainly concentrated in the northwest, northeast, and southeast, which are consistent with the distribution of industries and resources in the study area. This study can provide a reference for the precise prevention of HMs pollution of camphor and the safe selection of its pharmaceutical materials.