Variable-charge (v-c) soils in subtropical areas contain considerable amounts of iron/aluminum (Fe/Al) oxides that can strongly influence the fate of heavy metals in agricultural ecosystems. However, the relationship between heavy metal accumulation in vegetables and the geochemical factors associated with v-c soils in subtropical regions remains unknown. The present study investigated heavy metal accumulation under field conditions in the Pearl River Delta (PRD) by measuring the content of 8 heavy metals (zinc (Zn), arsenic (As), copper (Cu), mercury (Hg), lead (Pb), chromium (Cr), nickel (Ni) and cadmium (Cd)) in 43 pairs of v-c soil and vegetable (balsam pear and cowpea) samples. Soil physicochemical properties including pH, texture, organic matter and oxide minerals (Fe2O3, SiO2, Al2O3, CaO, MgO, K2O and Na2O) were also analyzed. Heavy metal accumulation from soil to vegetables was assessed based on bioconcentration factors (BCFs). The results showed that soil extractable Fe, oxide minerals and chemical weathering indices of v-c soils strongly affected heavy metal accumulation, whereas the content of Zn, Cu, Cr and Ni in vegetables was strongly affected by the soil clay content. Significant correlations were found between the BCFs of heavy metals and oxide minerals. However, no significant relationship was found between pH and heavy metal accumulation (except for Cu) in balsam pear and cowpea. Correlation analyses showed that a lower oxalate/DCB- extractable Fe content might indicate greater heavy metal (Zn, Cu, Hg, Cr and Ni) accumulation in vegetables. Therefore, it can be deduced that oxalate/DCB- extractable Fe content is a critical geochemical factor that determines the bioavailability of heavy metals and that iron biogeochemical cycles play vital roles in the fate of heavy metals in vegetable fields in this area. These findings provide new insights into the behaviors and fate of heavy metals in subtropical v-c soils and can be used to develop possible guidelines for vegetable safety management.