Background: Perceptions of school safety have an important effect on students' development. Based on the model of "context-process-outcomes," we examined school safety as a context variable to explore how school safety at the school level affected students' self-esteem. Methods: We used hierarchical linear modeling to examine the link between school safety at the school level and students' self-esteem, including school liking as a mediator. The data were from the National Children's Study of China (NCSC), in which 6618 fourth- to fifth-grade students in 79 schools were recruited from 100 counties in 31 provinces in China. Results: Multilevel mediation analyses showed that the positive relationship between school safety at the school level and self-esteem was partially mediated by school liking, controlling for demographics at both student and school levels. Furthermore, a sex difference existed in the multilevel mediation model. For boys, school liking fully mediated the relationship between school safety at the school level and self-esteem. However, school liking partially mediated the relationship between school safety at the school level and self-esteem among girls. Conclusion: School safety should receive increasing attention from policymakers because of its impact on students' self-esteem.