In the era of artificial intelligence, the rapid advancement of digital technology has led to its deep integration into university organizational learning systems, giving rise to the phenomenon of “mechanized” knowledge production. The metaphor of “university as a machine” enhances organizational learning efficiency through the “gear effect,” facilitating a shift toward diversified participation, open competition, and interactive learning. However, the mechanistic logic of “standardized input—programmed processing—efficiency-driven output,” when embedded in educational practices, risks eroding the essence of education. This may lead to the “gearing” of thought, manifesting in the decline of critical thinking, the technification of knowledge production, and the intensification of bureaucratic management. Thus, universities must transcend the limitations of the “machine” metaphor, striving for a balanced interplay between human agency and technological efficiency. This entails restoring individuals from instrumental roles to their rightful place as the true subjects of knowledge creation, thereby upholding the principle of human-centered education. In practice, a critical and reflective approach toward the “machine” metaphor is essential. Through a dialectical process of demystification, universities should anchor their efforts in value rationality, reconstructing a meaningful framework for governance. By adopting flexible governance structures, they can optimize organizational learning—preserving the order and efficiency of machine logic while safeguarding the authenticity and vitality of education.