A total of 4139 samples of agricultural soils were collected from the Shunyi District of Beijing to distinguish the natural and anthropogenic sources of heavy metals. The concentrations of heavy metals were detected in the soils, and their mean values followed a decreasing order: V > Zn > Cr > Ni > Cu> Co > Cd > Hg. The methods of multivariate statistical analysis were applied for source identification. It was determined that Co, Ni, Cr and V primarily originated from the parent material of the soils and that Cd, Cu, Zn and Hg were added primarily from agricultural cultivation. The CA also verified the PCA. Our research provides comprehensive approaches to better understand the potential sources in agricultural soils.