To enhance denitrification performance of soil infiltration, a soil infiltration system incorporated with heterotrophic denitrification (TSISHD) for urban runoff treatment was developed. Sawdust and grass powders were added in the anaerobic stage (ANS) to provide organic carbon sources for the denitrification process, and the reduction environment was improved by iron addition in the ANS. Aerobic respiration and nitrification primarily occurred in the upper aerobic stage (AES), which removed 86.68% of the chemical oxygen demand (COD) and 91.80% of the NH+4-N. Moreover, heterotrophic denitrification occurred in the bottom ANS when added sawdust and grass powders were used as a carbon source. Overall, the TSISHD showed remarkable removal efficiencies of 88.29%, 82.50%, 92.05%, and 78.10% for COD, NO−3-N, NH+4-N, and total phosphorus, respectively, and the corresponding effluent concentrations met the national quality standard of China for class V surface water. The removal efficiencies were significantly higher than those of the previous soil infiltration systems without inoculated microbes. The developed system has the potential to treat urban runoff.