It is important to evaluate the effectiveness of permeable pavements on flood mitigation at different spatial scales for their effective application, for example, sponge city construction in China. This study evaluated the effectiveness of three types of permeable pavements (i.e., permeable asphalts (PA), permeable concretes (PC), and permeable interlocking concrete pavers (PICP)) on flood mitigation at a community scale in China using a hydrological model. In addition, the effects of clogging and initial water content in permeable pavements on flood mitigation performance were assessed. The results indicated that in 12 scenarios, permeable pavements reduced total surface runoff by 1–40% and peak flow by 7–43%, respectively. The hydrological performance of permeable pavements was limited by clogging and initial water content. Clogging resulted in the effectiveness on total surface runoff reduction and peak flow reduction being decreased by 62–92% and 37–65%, respectively. By increasing initial water content at the beginning of the simulation, the effectiveness of total runoff reduction and peak flow reduction decreased by 57–85% and 37–67%, respectively. Overall, among the three types of permeable pavements, PC without clogging had the best performance in terms of flood mitigation, and PICP was the least prone to being clogged. Our findings demonstrate that both the type and the maintenance of permeable pavements have significant effects on their performance in the flood mitigation.