This longitudinal study employed a person-oriented approach to determine distinct latent groups emerge in social-emotional skills (SESk) when following the student participants from 7th grade to 9th grade in Finland. The latent transition of those groups was also examined. Furthermore, the motivation drivers (i.e., students' motivation toward three subjects learning and Phenomenon-based learning [PhBL]) behind the transitions were explored to understand the role of motivation in shaping social-emotional skills development. At 7th grade, 1362 students completed questionnaires on motivation, social-emotional skills, and well-being, with follow-up responses collected from the same participants two years later. The results indicated that three distinct SESk profiles (i.e., Low, Moderate, and High) were identified at both time points, and with curiosity and persistence emerging as the strongest differentiators among profiles. Latent transitions analysis showed that the Low- and High- SESk groups tended to converge toward the Moderate SESk group over time. When they aged, students classified into the High SESk profile were the most declined group, but the good news was low SESk group was going towards the middle; while moderate SESk group was the most stable ), with 73% of students remaining in the same level across time. We further found that students who experienced different motivation across multiple learning contexts (Finnish, Mathematic, Physics, and Phenomenon-based learning) in beginning of Grade 7 significantly predicted SESk profile membership and transitions. Phenomenon based learning was good for all profiles, but the cost was lowest. So, it was less stressful for them. For high SESk group, the cost is lowest in all subjects learning, that means subject learning is also a good context for them to develop SESk, becausee they don't need put that much efforts in cognitive learning. These findings have important implications for educational practices.