With the continuous enhancement of project safety management awareness, the traditional flood control mode relying on rainfall forecast or flow monitoring is encountering significant challenges. To address the issues existing in flood control and flood prevention work during the construction period of navigation and hydropower junction, such as scattered data, low sharing level, poor effect of flood evolution process, and weak ability of flood impact analysis, etc., in this paper, a multi-source heterogeneous standard intelligent flood control system database is established to achieve the unified management and sharing of data. An efficient and reliable flood evolution model is constructed, and the visualization and simulation of the flood evolution process are realized by integrating with the GIS spatial visualization engine. Based on the superimposition of sensitive flood control elements, the flood flow pattern, water surface line, and inundated range can be analyzed. The application in an navigation and hydropower junction project in the Minjiang River demonstrates that the research results of this paper can elevate the level of data management and sharing, strengthen the flood evolution simulation ability, enhance the flood emergency command and auxiliary decision-making ability, and provide technical support for the safe construction of the navigation and hydropower junction project during the construction period.