The flood discharge capacity and sediment transport capacity of WES weir and improved practical weir with polygonal line in a low-head hydro-junction are comparatively analyzed through physical model and mathematical model. The results indicate that the two types of weir both meet the requirements of norms and regulations for flood discharge in plain area. The discharge capacity of WES weir is better than that of the practical weir; whereas the improved practical weir is more beneficial for the normal operation of bulkhead gate and the safe running of the whole hydro-junction as it has intensified and wide weir surface turbulence, which will increase the sediment transport capacity and enable the sediment initiate easily, thus refraining from sedimentation to a certain extent. By comprehensive comparison, the improved practical weir with polygonal line is finally recommended.