Abstract: The problem of soil heavy metal pollution is becoming increasingly serious. Identifying the sources of soil heavy metal pollution has important guiding roles for pollution prevention and risk control. In this study, a concentrated distribution area of agricultural soils in the Pearl River Delta was selected to study the pollution characteristics and sources of heavy metals in soils by multiple methods including correlation analysis, elements distribution in soil profile, isotope ratio, principal component analysis and positive matrix factorization (PMF). The results show that the highest cumulative element in surface soil was Mercury (Hg), followed by Cadmium (Cd) and Zinc (Zn), and their average concentrations were 3.22, 1.29 and 1.09 times of the regional soil background values of the Pearl River Delta, respectively. The average concentrations of Arsenic (As), Lead (Pb), Chromium (Cr), Nickel (Ni), and Copper (Cu) were lower than the regional background values. The concentration of Hg in soil was only significantly positively correlated only with Pb, showing that Hg and Pb had the same sources. The obvious characteristics of surface layer aggregation of Hg and Pb in soil profile indicate the exogenous input. The combination of principal component analysis and stable isotope ratio can further identify the sources of Hg and Pb, which was highly correlated with the input of human activities such as industry and transportation. The results of PMF show that the accumulation of Hg and Pb in the soils of the study area was mainly caused by artificial sources such as industrial activities, and Cr and Ni in the soils were mainly from natural geological background, and Cd, Cu, Zn and As were greatly affected by both material migration and deposition from the upper drainage basin and natural geological background. When analyzing the cause of regional agricultural soil pollution, the rationality and reliability of the analytical results can be improved by the mutual verification of the combination using of different methods.