The aim of this study was to explore the role of self-esteem in the transition of adolescents among heterogeneous classes by using a three-wave survey conducted by the Taiwan Youth Project. A newly developed three-step specification latent transition analysis of Mplus7.3 was used for data analysis. The research variables were measures of self-esteem, scores on the dissatisfaction scale, depressive symptoms, and delinquent behaviors. A total of 2,685 junior high school students participated in the study, and self-report questionnaires were administered for three consecutive years. Latent profile analysis results revealed that the self-esteem of adolescents could be classified into four heterogeneous classes: low, middle, high, and contradictory classes. Latent transition analysis results also indicated that during the 3 years of the study, the transition of students from one class to another was more likely to be upward than downward. Furthermore, the ratio of movers from the seventh grade to the eighth grade was lower than that of movers from the eighth grade to the ninth grade. Auxiliary variables such as academic performance, peer relationship, closeness with homeroom teacher, and mother-child relationship exhibited a significant correlation with membership of the four self-esteem classes. Scores for distal outcomes such as depressive symptoms and delinquent behaviors were discovered to be significantly higher for low and contradictory self-esteem classes than their counterparts.