On the basis of the natural disaster comprehensive risk census data, this paper refines and constructs the vulnerability index of cultural relics protection units facing rainstorm disasters and establishes the indicator system for rainstorm disaster risk assessment of cultural relics protection units by comprehensively considering the three elements of rainstorm disaster risk, disaster-conceiving environment sensitivity, and cultural relics vulnerability. The rainstorm disaster risk and environmental sensitivity indicators are selected from the rainstorm risk level obtained from the census, which includes the rainstorm risk and environmental sensitivity of the disaster-conceiving environment, in which the rainstorm disaster-causing factors include the rainstorm process precipitation, the maximum daily precipitation, the maximum hourly precipitation, and the duration of precipitation from 1978 to 2020. The environmental impact factors of the disaster-conceiving environment include the standard deviation of the elevation, elevation, and the density of the river network, etc. The vulnerability of the cultural relics protection units includes the importance, exposure, sensitivity, and susceptibility of cultural relics. The vulnerability of cultural relics protection units includes three aspects of importance, exposure, and susceptibility, which includes eight indicators: protection level, affiliated cultural relics, area/scale, pedestal/(underground palace), cultural relics type, material type, deformation damage, and historical disaster. The reference weights of the indicators at all levels are given after the experts’ argumentation on cultural relics, meteorology, and emergency response. Based on the indicator system, the storm disaster risk of national key cultural relics protection units in Jincheng, Shanxi Province, is assessed and verified, and in the assessment, the weight of storm danger accounts for 75%. The eight cultural relics protection units with high storm disaster risk levels are all located in areas with high storm danger, among which the Xiangyu Ancient Fortress, the ancient architectural complex of Guobi Village, and the city of Miakovi are all located along the Qin River. The Shuitong Cui Fujun Temple, the Yuhuang Temple, and the Qinglian Temple are located along the Dan River, while the Tashui River ruins and Zezhou Dai Temple are located on the banks of the Tashui River and the Yedi River, respectively. The cultural relics protection units with a higher risk level are located in areas with a higher risk of rainstorms and at the same time have relatively high vulnerability. The research results provide a certain reference for the storm disaster risk assessment and protection of cultural relics protection units and at the same time enhance the application scope of the results of the comprehensive natural disaster risk census.