University autonomy is a strategic effort taken to realize professional service of universities. This research aimed to describe the implementation process of university autonomy and to find the model of autonomy implementation. The researchers utilized qualitative approach in the form of a case study using Spradley's technique of analysis. The results of this research presented that some universities in Indonesia have academic autonomy; Prabu Brawijaya University, Institut Teknologi Ganesha, and Kampus Bumi Siliwangi. The managements of the study programs and departments have autonomy in making policies for academic development. On the other hand, larger units of the universities make non-academic policies, i.e. the faculties at Prabu Brawijaya University, the faculties and the Directorate of Facilities and Infrastructures at Institut Teknologi Ganesha, and the faculties and the post graduate school at Kampus Bumi Siliwangi. It can be stated that the autonomy of universities in Indonesian just in semi autonomy level, for nonacademic affairs still cover by a higher unit. The implication is from the difference of academic and non-academic autonomy which affect the synergy decrement between academic program and non-academic support, so that the accomplishment in academic field cannot be optimum. The study program as the academic activity implementer needs to be supported by the authority of non-academic field for fulfiling the improvement of academic quality service.