The purpose of this study was to examine how university social capital and subjective social capital could predict undergraduate students’ subjective well-being including depression, school satisfaction, and life satisfaction. In this cross-sectional study, we conducted multilevel structural equation modeling on the data of 2,021 students at 38 universities in Japan. At the university level, we found the associations between social capital (fellows) and depression, social capital (classmates) and life satisfaction, and social capital (faculty) and school satisfaction. At the student level, all subjective social capital (fellows, classmates, and faculty) were associated with all the factors of subjective well-being. These results suggest the influence of university social capital and that of subjective social capital are associated with students’ subjective well-being.