Safety risk analysis and assessment of high-risk work system in hydroelectric project has an important role in safety management. The interactive relationships between human factors and the importance of factors are analyzed and proposed. We analyze the correlation relationship among the factors by using statistical method, which is more objective than subjective judgment. The HFACS is provided to establish a rational and an applicable index system for investigating human error in accidents; the structural equation modeling (SEM) and accident data are used to construct system model and acquire the path coefficient among the risk factor variables; the ANP model is built to assess the importance of accident factors. 289 pieces of valid questionnaires data are analyzed to obtain the path coefficient between risk factor variables and to build the ANP model’s judgment matrix. Finally, the human factors’ weights are calculated by ANP model. Combining SEM’s results and factor's frequency analysis and building the ANP model, the results show that the four greatest weight values of the factors are, respectively, “personal readiness,” “perception and decision errors,” “skill-based errors,” and “violation operations.” The results of ANP model provide a reference for the engineering and construction management.