In order to illustrate the influence of pipe system clogging and anti-backflow flap gate installation on urban hydrodynamic process, a coupling model of hydrologic and hydrodynamic was constructed based on the case study of a small catchment in the coast area of southeast China-Meixi Catchment. The coupling model is proved to be applicable. The simulation results show that the clogged conduits with the most adverse effect was identified spatially. For the degree of clogging, the conduits should not be clogged more than 20% of the inner diameter. With different return periods, the maximum inundation depth and peak time are not sensitive to clogging; however, it is not the case for inundation duration time in high return periods. In addition, when the anti-backflow flap gates are installed, the maximum inundation depth and the maximum inundation area will slightly reduce for each return period. More importantly, flap gate has played a positive role in reducing the inundation duration time. This study can provide technical support for flood forecast, conduits desilting and flood control management in Meixi Catchment.