The core of universities lies in colleges and departments, whose restructuring and reform has never stopped in China. Based on the analytical paradigm of historical institutionalism, this paper combs the historical changes of the basic administrative organizations in universities in China from the perspective of history, and finds that it has gone through four stages: forming stage, stage when it was compatible with academic organizations, disorder stage, and structure optimization stage. From the structural perspective, it probes into the basic institutional logic and the characteristics of the structural change of the basic administrative organizations in universities in China, and finds that it has four basic logical characteristics: rational return from imitating foreign countries to self-innovation, multi-party game from contradictions and conflicts to adjustments and compromises, intertwined development from gaps and interruptions to continuation and inheritance, and path turn from radical change to gradual interaction. There are four contradictions in it: making foreign things serve China and self-reliance, academic autonomy and administrative authority, the connotation-focused education and the ever-growing scale, and diversified disciplines and single administrative institution. We can reconstruct the basic administrative organizations in universities in China from four aspects: focusing on the transition logic with emphasis, constructing the coordinated transition logic, adhering to the dynamic gradual change logic, and constructing orderly governance logic.