With the rapid development of urbanization, heavy metal pollution resulting from runoff increase and vary greatly in different land use. However, there is still a lack of research on the risk assessment of heavy metal carried by the runoff. In Suzhou urban area, four land use types including commercial area, residential area, historical and cultural protection area, and cultural and educational area were selected to monitor the content of Cu, Zn and Pb in rainfall runoff. Further, the ecological risk of these three heavy metals was evaluated by risk quotient (RQ), which was on the basis of predicted no-effect concentration (PNEC) obtained by species sensitivity distribution (SSD) curve. Based on the event mean concentration (EMC) of six effective rainfall events, compared with the Environmental Quality Standard for Surface Water (GB 3838-2002), statistical results show that Zn and Cu in the rainfall runoff meet grade Ⅱ water quality standard, while Pb is inferior to grade V water quality standard, which are mainly affected by the traffic activities and roofing materials in different land use types. Correspondingly, commercial area is polluted by all these three heavy metals worst, the other areas are polluted in different degrees by different heavy metals, resulting in a large difference in toxicity to aquatic organisms. Generally, the ecological risks by heavy metals in rainfall runoff are in high-risk degree, and in the order of Pb > Cu > Zn. Therefore, the current environmental quality standard for surface water in China does not fully consider the ecological impact and underestimates the ecological risks of heavy metals.