It’s the first time to study the effect of soybean root exudate on microbial diversity. Maize and soybean root exudates enhanced the removal of PAHs at the early stage. After 10 days, a negative effect occurred for 160 mg TOC kg−1soybean root exudate. Bacteria community structure showed a complex interplay with soil and root exudates. The presence of root exudates increased the microbial diversity in agricultural soil.