This study analyzes the financial sustainability of Japanese public university corporations in a challenging environment characterized by a declining population and fiscal constraints. Utilizing Resource Dependence Theory, this study examines the “dependency,” “autonomy,” and “rigidity” of financial structures and their impact on financial sustainability. Using financial statements from 2004 to 2022, linear mixed models were applied to estimate growth trajectories over six-year medium-term goal periods, while categorizing universities based on the presence of affiliated hospitals. The results reveal that corporations without hospitals exhibit a high dependency on public funds and structural rigidity due to personnel costs. Furthermore, the linear mixed model analysis indicates a structural decline in ordinary income margins over time for these institutions. Conversely, corporations with hospitals show superficial stability; however, their financial risks may be inconspicuous owing to large-scale hospital operations. The study concludes that many public universities face a crisis of financial sustainability, characterized by “structural deterioration” where revenue diversification has not sufficiently progressed to offset rising costs.