Abstract: The Liangshui River is an important flood drainage channel for south flood diversion of Beijing. Although it has been treated for many times, there are still some water-blocking bridges which form bayonets and affect the safety of flood passage during flood seasons. Based on the MIKE11 model, this paper analyzes the flood prevention effects of the Wanquansi and Yongfeng Railway Bridges on the Liangshui River under the current river governance conditions. The results show that the water resistance ratio of the Wanquansi Railway Bridge and the Yongfeng Railway Bridge are 29.2% and 23.4%, respectively. The maximum backwater heights in the upstream are 0.206 m and 0.726 m, and the backwater lengths are 3498 m and 5136 m, respectively. The high water level will have certain impact on the discharge of coastal rainwater. The backwater caused insufficient clearance at the bottom of the Kaiyang Road Bridge, and the flooding of the river during the flood season affected the safety of the bridge. At the same time, the average flow velocity of the water-blocking bridge section increased by 0.23~0.84 m/s, resulting in intensified erosion of the channel and bank slope near the bridge piers, affecting the stability of the river bank.