Healthy development is not only about children’s physical health, but also involves mental health and social adaptability. In the preschool stage, the influence of multiple factors such as family, school and community has a profound impact on children’s health. In this paper, we used PLS-SEM combined with Bayesian network modeling to explore the mechanism of influencing factors on children’s health development in preschool education. The study first constructed a health influence mechanism model, taking into account the influence of multiple dimensions such as community environment, family support and school environment. The data of 600 preschool children were analyzed through a questionnaire survey and structural equation modeling was used to analyze the data. The results showed that four factors, namely, personal characteristics, community environment, family support and school environment, had a significant effect on children’s health, in which the direct effect of school environment was the largest, with a path coefficient of 0.305, and the direct effect of family support was the second largest, with a path coefficient of 0.221.The inference and diagnostic analysis of Bayesian networks revealed that changes in the school environment had a more significant effect on children’s health, especially when the children’s mental health and social adjustment are more negatively affected when the school environment is poor. The study suggests that children’s health development in preschool education is a complex system interwoven with multiple factors, in which the school environment plays a key role and requires special attention.