Though well-being problems are prevalent among PhD students, the contextual antecedents and underlying mechanisms behind these problems remain underexplored. The aim of this study was to explore whether and how the research environment affects the well-being of PhD students through their motivation. Self-determination theory was used as the theoretical framework in order to understand how the research environment plays a role in PhD students’ well-being. Students’ autonomous and controlled motivation was posited as mechanisms linking the research environment to well-being. PhD students (n = 2578) from eight Hong Kong government-funded universities were recruited. Results revealed various dimensions of the research environment including process and assessment, culture, and skills development that had distinctive connections with students’ motivation and their well-being. Furthermore, students’ motivation significantly mediated the relationships between the research environment and their well-being. This study provides theoretical implications for increasing awareness of the factors and mechanisms that support or undermine PhD students’ well-being. It also has functional suggestions for educators and administrators interested in enhancing PhD students’ motivation and well-being. Copyright © 2023 HERDSA.