Risk matrix analysis (LS) and operating condition risk analysis (LEC) have some limitations in rating the safety risks of water conservancy project, including unclear quantitative evaluation indicators, inconsistent criteria, and limited guidance for result application. In view of this, we developed a multidimensional and multi-spatiotemporal scale safety risk assessment system based on the risk matrix principle. Our research demonstrated the following outcomes: 1) the likelihood (L) of all types of hazard accidents in water conservancy projects can be assessed in detail by considering various combinations of control measures (M), frequency of hazard exposure (E), and working behavior (C) in the operation cycle. 2) The assessment criterion of M should be consistent with the standard of water conservancy project management. 3) The interaction between physical hazards evolution and environmental change can be assessed through the risk assessment factor C. 4) In consideration of the unbalanced spatiotemporal distribution of accident consequences, the safety risks of water conservancy projects can be assessed dynamically by incorporating the upstream water level (H) and operation period (F) and identifying whether hazard sources are directly related to downstream flood control or the casualties and economic losses caused by accidents can be quantified. This dynamic and real-time evaluation approach for water conservancy project safety risks offers a valuable reference for constructing a double prevention mechanism for safe production in the industry.