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Source quantification of heavy metals in farmland is essential for developing and implementing restoration strategies. We used various data analyses to identify and quantify sources of arsenic, cadmium, chromium, copper, mercury, nickel, lead, and zinc in vegetable-growing soils. A new method of collaborative assessment, combining soil environmental quality and agricultural product safety, showed that approximately 5.20% of cultivation systems were multi-contaminated by heavy metals. The nonlinear relationship between pollution sources and the comprehensive contamination situation was established, deriving from a fitted bivariate model. The model revealed that anthropogenic sources and natural origins accounted for 65.8–86.0 and 34.2–14.0% of the comprehensive pollution, respectively. These results suggested that both human activities and natural factors contributed to the decline of local soil quality and the influence of the former was more substantial than that of the latter.