The water conservancy project is an important livelihood engineering project, and it is also an important factor to ensure the living water supply, power supply stability, and economic development of the regional population. Therefore, the management of water conservancy projects is particularly important. The core management content is cost control, which can maximize the benefits of the project and avoid the waste of investors’ funds. This study studies the whole process control of water conservancy project cost, explains the problems existing in the current domestic water conservancy project cost control, and finally expounds on the whole process control measures, in order to provide a reference for related work. In this study, SPSS software is mainly used to establish a multiple linear regression model to analyze the influencing factors of water conservancy projects. Through the method of model solving, the relationship between hydraulic engineering and various variables is analyzed, and the multi-linear verification is improved, so as to further test the model, optimize the model, and finally manage and predict it accurately.