Abstract: The construction of waterway channelization project not only raises the navigation level of waterway, but also brings the hidden danger to ship navigation. The inland waterway in mountainous area is affected by the irregular discharge of the upstream power stations and the rainstorm confluence in the basin, which often results in the sudden rise of the water level in the downstream waterway, the surge of the velocity and the complexity of the flow pattern, and so on. To this end, a set of advanced scientific water safety prediction and early warning system has been developed. Based on the field real-time data acquisition and historical hydrological data, the system can analyze the hydrological correlation between the channel topography and the monitoring stations in the upper and lower reaches, and the hydrological mathematical prediction model including water level, velocity and discharge was established, which realized accurate, timely, effective hydrological monitoring, forecasting and early warning. The system has been verified and demonstrated in Fuling section of the Wujiang River. The results showed that the monitoring data of the system is accurate, and the accuracy of prediction results met the requirements. The system is of great significance to the navigation control, flood control and emergency disposal of inland waters, especially mountainous rivers.