Nowadays, heavy metal pollution in soil caused by human production activities is increasingly serious. The heavy metal ions in soil inhibit plant growth and endanger human health as they can disrupt the physicochemical properties of soil. However, the elimination of heavy metals in soil is so difficult that more and more researchers are studying effective soil conditioners. The negatively charged groups in microbial communities can bind with heavy metal ions in the soil to remove them. In this paper, Cr- and Cd-polluted soils were used to simulate heavy-metal-polluted soil, and microbial compound fertilizer (MOF) was used as a soil conditioner for removing Cr and Cd in soil. The effects of different additive amounts of MOF on the physicochemical properties, the concentration of metal binding forms in soil and the enzyme activity of soil were investigated. The results showed that when the addition amount of fertilizer was 10%, the improvement effect on Cr- and Cd-polluted soils was the best. Compared with polluted soils without MOF addition, the physicochemical properties of MOF-treated polluted soils improved significantly, the concentration of effective forms of heavy metals decreased significantly, and the concentration of organic and residual forms as well as soil enzyme activity increased significantly. This indicates that the addition of MOF can increase the activity of soil microbial communities and soil fertility, and has the ability to remediate heavy-metal-polluted soil. MOF is expected to become an efficient soil conditioner for heavy metals.