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Despite the prevalence of well-being issues among PhD students, the contextual factors and mechanisms underlying these problems are not well understood. This study investigated how the research environment affects PhD students’ well-being through their motivation, using self-determination theory as a framework. Data from 2,578 PhD students at eight Hong Kong universities revealed that various aspects of the research environment, including process and assessment, culture, and skills development, had distinct relationships with students’ motivation and well-being. Students’ motivation significantly mediated the relationship between the research environment and well-being. The findings provide theoretical insights into factors influencing PhD students’ well-being and offer practical suggestions for educators and administrators to enhance students' motivation and well-being in doctoral programs.