Teachers' motivation, which pertains to the reasons to sustain teaching, plays a pivotal role in shaping students' learning motivation, school engagement, and academic achievement. However, the relationship between teachers' motivation and students' emotional well-being remains unclear. This study, grounded in self-determination theory and the prosocial classroom model, investigated the associations between teachers' autonomous motivation and controlled motivation with students' emotional well-being and examined the potential mediating role of students' perceived teacher-student relationships and teacher support in these associations. The current study involved 49 homeroom teachers and 1853 students, assessing teachers' autonomous motivation, controlled motivation, students' perception of teacher support, teacher-student relationships, and emotional well-being. The results of the multilevel analysis indicated that (1) teachers' autonomous motivation positively predicted students' emotional well-being, mediated by teacher support; (2) teachers' controlled motivation negatively predicted students' emotional well-being, mediated by both students' perception of the student-teacher relationship and teacher support. The findings underscore the significance of intervening in teachers' work motivation, particularly controlled motivation, in educational and teaching practices to improve students' mental health.