Adding compost to degrade acetochlor in soil is an important way to reduce its impact on the environment. The addition of conditioner improved the generation of compost products with specific effects. Thus, in order to determine a better composting conditioner for degradation of acetochlor, the dissipation of acetochlor in unmodified and different composting conditioners (zeolite, biochar, zeolite + biochar) was studied by pot experiment. The effects of residual concentrations of acetochlor (1.02, 1.56 and 2.08 mg·kg−1) and soil types (phaeozem and stagnic soil) on the dissipation of acetochlor were evaluated. The community structure of microbial fungi and bacteria in soil was determined by high-throughput sequencing to evaluate the change of microbial community in the soil with acetochlor residue. The results showed that compost types, soil types and the concentration of acetochlor residue in soil had different effects on the dissipation of acetochlor in soil. The addition of biochar and zeolite could significantly increase the degradation rate of acetochlor in soil. When the same compost was added, the degradation of acetochlor was fastest in phaeozem with a degradation rate of 95.13%. The degradation rate of acetochlor in black soil was higher than that in stagnic soil. High throughput sequencing results showed that the application of organic fertilizer changed the structure of soil microbial community. Luteibacter, Sagenomella and Remersonia had the highest correlation with the degradation of acetochlor in soil. The analysis of microbial community showed that·Luteibacter (24.49%),·Sagenomella (1.55%) and Remersonia (3.14%) played important roles in the degradation of acetochlor. Artificial neural network analysis showed that the sensitivity of acetochlor degradation rate to the conditioner in the soil was biochar (60.07%) > biochar + zeolite (21.19%) > blank (13.97%) > zeolite (4.77%). These results showed that biochar compost was more conducive to the dissipation of acetochlor in soil after application, and the application of organic fertilizer affected the soil microbial community structure.