In the water shortage countries and areas, untreated sewage irrigation led to the extensive organic pollution of farmland soil, which seriously threatened environmental security. In this study, we selected Shenfu irrigation area (SIA) as the study area, and it was the first and largest organic sewage irrigation area in China. We analyzed the temporal and spatial variations in concentrations, risk and sources of polycyclic aromatic hydrocarbons (PAHs) in soil of the SIA. The results show that the PAH concentrations decreased slowly and environmental risk fluctuated after stopping sewage irrigation. However, the correlation and divergence analysis indicate that PAHs in surface soils might be derived from traffic emissions besides sewage irrigation. Based on factor analysis with non-negative constraints, the contribution of irrigation decreased from 92.9% to 59.4%, and contribution of traffic increased from 7.1% to 40.6%. Thus, the superposition of the residual PAHs from sewage irrigation and the new input PAHs from traffic emission should be considered for the pollution control.