[Objective] The flood risk evaluation in medium and small basin caused by urbanization were carried out in East and West Stream watershed in Xiamen City in order to provide some references for the flood control and disaster mitigation in study watershed. [Methods] Based on the spatial analysis of GIS and the two-dimensional hydrodynamic model named MIKE21, the flood risk analysis and submerged conditions were simulated by the combined rainstorm flood frequency analysis and plain flood submerging model. [Results] The dynamic flood hazard map of the East and West streams watershed in Xiamen City was created, together with the current land use change condition, the instant flood hazard map is able to establish according to the flood frequency. [Conclusion] The flood risk in the study area was mainly distributed in the main stream of the East stream, West stream and Ting stream watershed. With the increase of the flood recurrence period, the flood hazard tends to increase from upstream to downstream and from near-shore to off-shore.