Stepped bioretention systems have been increasingly used for rainwater treatment in hillside areas. However, the depth of aquifer and soil permeability coefficient limit the treatment effect of runoff rainwater, resulting in a large amount of overflow water, particularly during extreme rainfall events. Here, in contrast to the ordinary stepped bioretention system (OSBS), an improved stepped bioretention system (ISBS) was developed by changing the overflow channel and the inflow and overflow were analyzed under various rainwater conditions. ISBS has high stability and the ability to control runoff rainwater. The runoff rainwater volume reduction rate reached 51.5–100% and the removal rate of suspended solid, chemical oxygen demand, total phosphorus and total nitrogen were 31.2–47.9%, 27.1–51.7%, 26.5–59.0% and 26.7–46.9%, respectively. According to the working principle of the continuous stirred tank reactor (CSTR), the permeable water concentration of other rainfall events can be predicted by using the parameters obtained from extreme rainfall events. In general, ISBS is a very promising runoff rainwater treatment technology, which can reduce the overflow quantity and recharge groundwater under various rainwater conditions.