Interdisciplinary training for doctoral students is an emerging scenario in higher education. The learning relations of knowledge transfer (KT: transferring knowledge from one person to another) and knowledge integration (KI: integrating or synthesizing perspectives from different disciplines) built by doctoral students play an important role in the process of interdisciplinary training. This study explores how doctoral students from a wide range of disciplines build learning relations of KT and KI during online interdisciplinary training. A mixed-methods approach was applied. First, longitudinal social network analysis (SNA) was employed to investigate the patterns of KT and KI relations over a seven-month training period. Subsequently, interviews were conducted to triangulate the SNA findings. SNA results show that the establishment of KI relations is significantly less than that of KT. Qualitative results show three themes explaining the challenges of KI relations, including challenges of online settings, the design of the training modules, and student involvement. Practical implications are drawn for the improvement of online interdisciplinary training, such as suggestions to promote KI and strategies for group learning.