Abstract: The impact of pesticide on soil microorganisms is an important index to evaluate ecological safety of pesticides. Procymidone is widely used fungicide in China, but its effect on soil micro-ecosystem has not been studied yet. Illumina sequencing technology was used to evaluate the effects of procymidone on soil microbial diversity. By comparing the species annotation results of soil contaminated by procymidone with control soil, we found that usage of procymidone significantly reduced organism abundance and diversity of the soil microorganism. In the control soil, Candidatus Brocardias is the dominant genus and Candidatus Brocardia sinica is the most dominant specie. While in the procymidone contaminated soil, the dominant genus is Stenotrophomonas and the most dominant specie is Stenotrophomonas maltophilia, which shows strong drug-resistance. Moreover, according to the genetic function annotation results, the abundance of genes involved in nitrification and sulfate reduction is significantly reduced whereas the abundance of drug-resistant genes is significantly increased in procymidone contaminated soil. Therefore, procymidone has significantly changed the structures of microorganism community in soil by increasing drug-resistant community and decreasing the nitrifying community. This study provides theoretical value on evaluating the ecology safety.