Against the background of China’s doctoral recruitment system shifting from scale expansion to quality orientation, the institutional logic and operational effectiveness of doctoral admissions have come under continuous attention. Taking International Relations as a disciplinary entry point, this study selects Tsinghua University and Peking University in China, together with the University of Tokyo and Kyoto University in Japan, as comparative cases. Through institutional document analysis, the paper examines the organizational structure, selection procedures, and decision-making mechanisms of doctoral admissions in International Relations across these universities. The findings indicate that Chinese universities place stronger emphasis on procedural standardization and comparability, relying primarily on centralized institutional arrangements and document-based evaluation to complete the selection process. In contrast, Japanese universities depend more heavily on laboratories or research units and faculty judgment, positioning research fit at the core of admission decisions. These differences reflect institutionally embedded choices shaped by disciplinary structures, configurations of academic communities, and state–university relations.