In school-to-university transition literature, autonomy has been implied or explicitly explained as an important factor to predict the persistence and engagement of students in higher education; however, little qualitative research addresses students' transition in relation to autonomy, what these students have to go through in terms of becoming more independent in their studies and life in university, nor how they manage to live up to the expectations and standards. For this longitudinal qualitative study I investigated the major issues of 9 mainland Chinese students during their first year in a Hong Kong university from the perspective of learner autonomy. The data were collected across 1 year through different methods. Findings of the study reveal that the major issues the students encountered challenged and developed their autonomy in management of personal life and learning. Understanding how autonomy underpinning the complexity of students' academic and social transition enables teachers, educators, and policy makers to modify their practices accordingly.