<p>Higher education is under increasing pressure to address complex ecological challenges and growing societal demands, making the cultivation of interdisciplinary talent a vital mission. Interdisciplinary learning at the graduate level is regarded as research-oriented, cross-disciplinary, collaborative learning that differs significantly from its orientation at the undergraduate level. This study analyzes the factors influencing two interdisciplinary learning structures on the learning outcomes of interdisciplinary graduate students in Taiwan and Japan through a survey of representative universities in both countries. The findings illustrate that achievement assessment and learning engagement play crucial roles in the interdisciplinary learning outcomes of students from these universities. Notably, we find that departmental learning engagement negatively affects interdisciplinary learning outcomes. These results highlight the importance of epistemology in interdisciplinary learning. How students understand the course content and interact with other disciplines is critical to their success in interdisciplinary learning. This study reveals key gaps in interdisciplinary learning studies in East Asia and contributes to the development of future research.</p>