A tub experiment was conducted to investigate the effects of humic acid and potassium polyacrylate on soil biological diversity under heavy metal lead (Pb) and cadmium (Cd) pollution, in which 600 mg/kg of Pb and 1.8 mg/kg of Cd were added into all tubs (T2), then 10 g/kg of cottonseed meal humic acid (T4), 2 g/kg of polyacrylic acid potassium (T6), the combination of T4 and T6 (T8) were added into the tubs, respectively. Soil microbial biodiversity was analyzed by high-throughput sequencing and the remediation response was studied by Fourier transform infrared spectrum. The results showed that the contents of Cd and Pb in the topsoil were reduced in the treatments of T4, T6 and T8, the maximum reduction occurred in T8, which were 62.6% for Cd and 52.3% for Pb, respectively, thus, it changed soil micro-environment and thus affected soil microorganisms. The bacteria in the four treatments covered 25 phyla, 69 classes, 149 orders, 273 families and 442 genera, and Proteobacteria, Acidobacteria, Gemmatimonadetes and Actinobacteria were the dominant bacteria. T6 increased the total number of Proteobacteria, while T4 and T8 increased Acidobacteria and Gemmatimonadetes. It can be concluded that the microbial diversity was very rich and the dominant bacterial community was relatively stable in Cd and Pb polluted soil. Potassium polyacrylate and cottonseed meal humic acid affected composition abundance of bacterial flora by changing soil microenvironment.