Against the backdrop of a deepening digital economy and educational transformation, structural challenges, including rigid approval processes, a lack of collaborative mechanisms, and weak data governance, severely constrain administrative efficiency in higher education institutions. The core issue lies in the dual imbalance between insufficient technological support and rigid process design. Grounded in the theoretical framework of modern educational governance, this study constructs a comprehensive framework encompassing “theoretical foundation, dilemma deconstruction, mechanism analysis, and path prevention.” It systematically examines the manifestations, causes, and practical impacts of three major dilemmas, elucidates three synergistic mechanisms for integrating intelligent technologies with office workflows—two-way adaptation, service enhancement, and management quality improvement—and proposes actionable strategies such as “routine-first special-case” categorized policies, “easy-first difficult-later” platform development with lightweight safeguards, and tiered risk prevention. The research provides theoretical support and practical guidance for digital transformation in university administration, significantly contributing to the advancement of scientific and intelligent management practices.