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Previous research has underscored the importance of motivation in PhD students’ development. However, little attention has been given to understand motivational profiles among PhD students. This latent profile analysis (LPA) analysis pioneered PhD students’ research motivation profiles and their relationships with research agendas. Using a sample of 351 PhD students (Mage = 29.9, SDage = 4.48; 60.97% females) from 15 universities in mainland China, three distinct profiles were found based on the LPA: demotivated, averagely motivated, and strongly motivated. Profiles with higher motivation were more valuable to research agendas, especially innovative agendas. This study provided significant theoretical contributions and practical implications for PhD education.