Pesticide contamination has emerged as a global threat to humans. Here, we investigate the soil distribution pattern of organic phosphorus pesticide contamination at a pesticide manufacturing site in northern China, exploring their relationships with soil properties and microbial communities. The concentrations of four organic phosphorus pesticides (i.e., phorate, terbuthion, fenitrothion, and parathion) decreased substantially with soil depths from the surface down to 2 m. However, terbuthion, fenitrothion, and parathion had second-peak concentrations at a depth of 8 m. The concentrations of those organic phosphorus pesticides were negatively correlated with soil water content, but positively correlated with sulfide, pH, and total phosphorus. The distribution patterns of organic phosphorus pesticides closely aligned with that of soil organic matter and clay minerals, especially in the presence of montmorillonite, kaolinite, and chlorite. Various bacterial genera known to degrade organic phosphorus pesticides, such as Flavobacterium, Bacillus, Acinetobacter, Lactobacillus, Pseudomonas, Sphingomonas, and Thiobacillus, were correlated with these pesticides. Since these genera were among the top 50 abundant genera in our samples, they might play a significant role in the degradation of organic phosphorus pesticides. Together, this study unveils previously unrecognized pesticide-soil-microbe interactions, thus providing an important knowledge basis for environmental remediation strategies.