•Humic acid residue (HAS) is currently a wasted resource.•We modified HAS with NH4H2PO4 to improve its heavy metal stabilization capacity.•N-HAS reduces the mobility of Hg and Pb in soils.•Addition of N-HAS alters soil physicochemical properties.•N-HAS was an industrially produced heavy metal passivator. Humic acid residue (HAS), as a waste product from the extraction of humic acid from low-rank coal such as weathered coal and lignite, is characterized by its abundant yield and low price. However, the low efficiency and high pH value of HAS in passivating heavy metals limit their application in the passivation of heavy metals in soils. To improve the passivation efficiency of humic acid residues against heavy metals, in this study, modified humic acid residues (N-HAS) were prepared by pretreatment with HNO3 and modification with NH4H2PO4. The results showed that the passivation efficiency of N-HAS was up to 87.75% and 57.07% for Hg and Pb in the effective state, and the adsorption kinetics were under the pseudo-second-order model. The addition of N-HAS to the soil resulted in a change in the morphology of the heavy metals, with the acid extractable state of Hg and Pb reduced by 66.92% and 30.44% respectively, and the results of the Toxicity Leaching Test (TCLP) showed that the addition of N-HAS significantly reduced the leaching toxicity and potential ecological risk index (RI). The soil physicochemical properties changed after the addition of N-HAS and there was a correlation between the soil physicochemical properties and the effective state of Hg and Pb content. In conclusion, N-HAS has a positive effect on the remediation of heavy metal-contaminated soil and has a broad application prospect.