Sulfidation effectively improves the electron transfer efficiency of nanoscale zero-valent iron (nZVI), but decreases the specific surface area of nZVI. In this study, sulfidated nZVI (S-nZVI) coated with rhamnolipid (RL-S-nZVI) was synthesized and used to stabilize Pb, Cd, and As in combined polluted soil. The stabilization efficiency of 0.3% (wt) RL-S-nZVI to water soluble Pb, Cd, and As in soil reached 88.76%, 72%, and 63%, respectively. Rhamnolipid coating inhibited the reduction of specific surface area and successfully encapsulated nZVI, thus reducing the oxidation of Fe0. The types of iron oxides in RL-S-nZVI were reduced compared to S-nZVI, but the content and strength of Fe0 iron were obviously enhanced. Furthermore, rhamnolipid functional groups (-COOH and -COO-) were also involved in the stabilization process. In addition, the stabilization efficiency of RL-S-nZVI to the bioavailable Pb, Cd, and As in soil increased by 41%, 41%, and 50%, respectively, compared with nZVI. The presence of organic acids, especially citric acid, improved the stabilization efficiency of RL-S-nZVI to the three metals. The result of BCR sequential extraction indicated that RL-S-nZVI increased the residual state of Pb, Cd, and As and reduced the acid-soluble and reducible state after 28 days of soil incubation. XRD and XPS analyses showed that the stabilization mechanisms of RL-S-nZVI on heavy metals involved in ion exchange, surface complexation, adsorption, co-precipitation, chemisorption, and redox.