As densely populated social organizations, universities hold special governance value in emergency response mechanisms during public health events. Through qualitative research methodology and NVivo 15 analysis, this study systematically analyzes the epidemic prevention and control notification documents issued by 17 Ministry of Education-affiliated universities in the Yangtze River Delta region. Findings reveal fourfold deficiencies in formal legality of university emergency regulations: structural imbalance in legislative basis, unilateral decision-making procedures, inadequate formal requirements, and asymmetric allocation of rights and responsibilities. At the substantive legality level, three value conflicts emerge: disconnection between the legitimacy of prevention goals and the rationality of measures, absence of protective legal provisions, and instrumental rationality expansion in institutional ethics. To address these issues, improving normative foundations, strengthening procedural justice, and balancing value orientations are recommended to enhance the legitimacy of university public health emergency prevention policies and elevate the rule-of-law standard in university emergency management.