The small urban watershed storm runoff model of mountain city, which bases on the hydrological method and ArcEngine extension programming was developed aim at stimulating the flood situation, locating the flooding area, computing the subsiding time of flood, utilization and management of the stormwater through the rainfall data. The model was used in Panxi basin of Chongqing. The simulated situation showed that the Nash-Suttcliffe coefficient Ens is 0.56-0.76, the relatively error is 8.82%-11.8%. According to the parameter sensitivity analysis the most sensitivity parameters of the model are width of subcatchment, slope, manning coefficient and impermeable area rate. The model had analyzed the flow, full degree and number of overflowed wells to evaluate drainage capability of drainage system. Results showed that 0.52% of the drainage pipes were overload under one-year storm; compared with 5.86% and 8.20% under fifty-year storm and one-hundred-year storm respectively. By comparing the flow depth inside the wells with the placing depth the assessment results showed that 0.72% of the wells had spillover under one-hundred-year storm and 0.31% of the wells had spillover under one -year. Overall the model achieves effective management of storm runoff and assessment of the water drainage system capacity in mountainous city.