With the deepening of urbanization, increasing attention has been paid to the status quo and control of heavy metal pollution in soil; however, identifying pollution sources is the premise of effective pollution control. Source analysis has been widely used to evaluate heavy metals in environmental receptors. In this paper, the common methods and principles of source analysis of soil heavy metals pollution in recent years are summarized, and a system combining various methods is proposed. A typical farmland in the Pearl River Delta was selected as a case area. The results indicated that (1) concentrations of Cd, Pb, Cu, Zn, and As in some soil samples were greater than the filter capacity of agricultural land according to the Soil Environmental Quality of China, especially cadmium, which reached 60.1%; and (2) the accumulation of heavy metals in soils was related to the overuse of fertilizers for industrial production, traffic pollution, and soil parent material. (3) The results of the correlation analysis implied that the r² values of Cd, Ni, Zn, and Hg were more than 90%, and the r² values of other heavy metals were more than 60%, which indicates that there were significant correlations between the values of the measured and predicted heavy metals. (4) The contribution rates of the sum of transportation and agriculture to soil Pb accumulation through the PMF model and Pb stable isotope ratio method were 86.0% and 84.8%, respectively. The contribution rates of agriculture to soil Cd through the PMF model and material flow analysis were 86.7% and 79.7%, respectively. (5) The results indicate that the positive matrix factor, isotope ratio analysis, and material flow analysis methods can be well combined to study the source of heavy metals in soil.