Heavy metals are the primary pollutants in agricultural soil and have hindered the sustainable development of agriculture. To control heavy metal pollution, it is essential to identify the pollution sources, particularly the prior source, in agricultural soils. In the current study, Qianguo Irrigation District, a typical agricultural region in Northeast China, was selected to be investigated for the source apportionment of soil heavy metals and identify the prior pollution source. The results showed that the study area was at a moderate pollution level with considerable ecological risk, while Hg and Cd were the main pollutants. Human-health risk assessment indicated that the non-carcinogenic risk for all populations was acceptable (HI < 1), and the carcinogenic risk was not negligible (10⁻⁶ < TCR < 10⁻⁴). The main pollution sources were concluded to be of lithogenic origin (35.5%), livestock manure (25.4%), coal combustion (21.5%), and chemical fertilizers (17.7%). Coal combustion was identified as the prior pollution source, accounting for 47.69% of the RI contribution. This study can provide scientific support for environmental management and pollution control of soil heavy metals in agricultural regions.