In order to explicit the environmental activity of heavy metals affected by different organic acids in soil, a batch incubation experiment was explored to investigate the influence of high relative molecular mass organic acid (HMWOA) (humic acid and fulvic acid) and low relative molecular mass organic acid (LMWOA) (threonic acid and oxalic acid) on the release or immobilization of Pb, Cu and Cd in soils. Results showed that LMWOA, especially threonic acid, had a good performance in the release of Pb, Cu and Cd from soils, and decrease in the fractions of HOAc-extractable, reducible and oxidable Pb, Cu and Cd. Conversely, HMWOA, especially humic acid, decreased the release of Pb, Cu and Cd, while it increased the fractions of HOAc-extractable, reducible and oxidable Pb, Cu and Cd, indicating that HMWOA can immobilize heavy metals. The release of Pb, Cu and Cd caused by LMWOA was attributed to the dissociation of soil organic matter and amorphous iron oxides since the total organic carbon and the water-soluble iron increased. The immobilization of Pb, Cu and Cd by HMWOA was attributed to the adsorption onto HMWOA followed by amorphous iron since HMWOA resulted in a significant decrease of zeta potential and an increase of amorphous iron oxide. It can be concluded that LMWOA has a potential application in soil washing remediation, while HMWOA can be used in the immobilization remediation for heavy metals contaminated soils.