Owing to the frequent accidents in primary and secondary schools (PSS) in China in the past decades, a systematic analysis of indicators influencing safety risks in PSS is critical to identifying preventive measures. A two-hierarchy structure of indicators was identified by analyzing various cases, intensive interviews, and related previous literature. A combination of the analytic hierarchy process and the entropy weight method was developed to synthetically assess the primary and secondary risk indicators through a case study of Ma Shan School in China. The results are as follows: (1) the primary risk indicators, namely, natural disasters, public health, facility safety, accidental injury, public security, school bullying, and individual health constitute the evaluation framework of the safety risks in PSS. (2) Public health risks and accidental injury risks are the most critical factors that should be prioritized. In addition to providing academic implications, several managerial implications are proposed for these stakeholders to reduce the safety risks in PSS.