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 management control. A concentrated distribution area of agricultural soils in Chongqing was selected to study the pollution characteristics and sources of heavy metals in soils by multiple methods including geo-accumulationindex，pollution loadindex，correlationanalysis，principal component analysis and positive matrix factorization. The results showed that the average concentrations of heavymetals(Cd，Hg，As，Pb，Cr，Cu，Zn andNi)in the surface soil all exceeded the soil background value inChongqing，showing different levels of enrichment. The highest cumulative element in surface soil wasHg，followed by As andCd，and their average concentrations were54.70，3.03，1.50 times of the soil background values of the Chongqing. The statistical results of the geo-accumulation index indicated that Hg and As were pollutants in the study area with a high pollution level. The evaluation results of the pollution load index method showed that the study area was slightly polluted as awhole，and thecomprehensive pollution loadindex( Pzone)of the study area was 1.76. The results of positive matrix factorization showed that the accumulation of As and Pb in the soil of the study area weremainly caused by industrial activities and trafficemissions，andCr，Cu，Zn and Ni in the soils weremainly from natural geologicalbackground，and Cd in the soils was mainly causedby agricultural productionactivities，and Hg in the soils was mainly caused by mining of mercury ore.