Green roofs are a new measure to control city nonpoint source pollution. The objective of this study was to examine the effects of substrate depth and biochar on the capacity of green roofs to intercept rainfall and reduce pollution in runoff. The amount and water quality of rainfall and the runoff from asphalt roofs (AR) and green roofs with or without biochar substrate were measured for 93 rainfall events. The substrate depth significantly increased the green roof runoff retention rate, while it did not significantly affect the concentration of water quality parameters in the runoff. The addition of biochar to the substrate could increase the retention rate of green roof runoff and could significantly reduce the electrical conductivity (EC) and concentrations of TN, NO₃^–-N, NH₄ ⁺-N, COD, TOC, K⁺, Ca²⁺, Cl^–, SO₄^2–, Fe and Zn in the green roof runoff, however, biochar increased the concentration of TIC in the runoff. Notably, the addition of biochar to the green roof substrate prominently reduced the pollution load of TN, COD, and NO₃^--N in the runoff and therefore it was as a sink. The main pollution sources of green roof without biochar substrate were organic, ion, nutrient, physicochemical, and metal pollution. However, from the green roofs with biochar substrate, the pollution sources were severely affected by biochar and mainly were organic and metal, ion, nutrient pollution, and biochar. These results provide a scientific basis for the design and application of green roofs to manage and control urban storm runoff.