With the deepened practice of the policy for “easing the burden of excessive homework and off-campus tutoring for students undergoing compulsory education,” more attention is paid to students’ well-rounded development and wellbeing. To explore how school principals and teachers affect students’ school wellbeing so as to create a good educational ecology for schools, improve the people’s satisfaction with education, and offer effective and evidence-based approaches to the rapid construction of a high-quality education system rooted in China’s reality, this study explores the effect of school principals’ instructional leadership on students’ school wellbeing, based on data from the “Investigation of Curriculum and Instruction in China (ICIC)”, which covers 53 representative secondary schools from a certain province in central China. The authors find the following: The school principals’ instructional leadership has direct and indirect effects on the students’ school wellbeing, and teachers’ teaching self-efficacy and the teacher-student relationship play a chain-mediating role. To enhance students’ school wellbeing, we need to improve school principals’ instructional leadership to stimulate teachers’ teaching self-efficacy and promote the construction of a positive teacher-student relationship. This provides effective and evidence-based approaches and mechanisms for the effect of school principals on students’ school wellbeing through their instructional leadership, and offers preliminary enlightenment to the promotion of the high-quality development of education rooted in China, and the exploration into the active role of empirical research in the identification of the “reason” behind the wisdom of China’s educational practice.