The purpose of this study was to identify the challenges of cyberspace governance in Iranian universities from the perspectives of three key stakeholder groups: university administrators, students, and communication experts. The main research question was: What are the primary challenges of cyberspace governance in the university context, and how do these challenges emerge through the interaction of stakeholders’ viewpoints? The research adopted a qualitative approach using thematic analysis. Data were collected through semi-structured interviews with 21 participants (7 administrators, 8 students, and 6 communication experts) from three public universities in Bandar Abbas, Minab, and Qeshm, and were analyzed using MAXQDA 2022 software. The findings revealed four main themes: (1) cultural-identity barriers stemming from the tension between academic identity and the security-oriented institutional framework; (2) structural-institutional barriers resulting from institutional fragmentation and policy incoherence; (3) technological barriers** arising from inadequate infrastructure and a shortage of skilled personnel; and (4) individual barriers driven by administrators’ control-oriented mindset and students’ sense of digital insecurity. The central conclusion is that cyberspace governance in Iranian universities is not primarily a technical issue, but rather a structural-identity crisis that requires a fundamental rethinking of the conceptual framework of digital governance.