Developing learner autonomy (LA) requires a shift of control from teachers to students. This development also relates to teacher autonomy (TA), which requires school managers to relinquish some degree of their own autonomy (MA) to teachers. Thus, a problem arises: how can the three levels of control-shifts co-exist and survive in harmony, and ideally, thrive each in its own way? Based on a recent case study, this paper aims to explore the complexity of the dynamic interaction between these three types of autonomy within an educational hierarchy. The study was conducted in a Chinese secondary school which was promoting whole-person development through a comprehensive innovation project. The participants comprised nine English teachers, the executive director, and the principal. Data collection methods included interviews, observations, and post-lesson discussions. Three issues are addressed in this paper: the principal ’s perceptions of LA, a classroom instruction model to cultivate LA, and a teacher training scheme to facilitate TA. The findings display a complex picture of these issues, and imply the importance of a genuine, shared understanding of the nature of autonomy and the need to carefully ensure the optimal balance among the three types of autonomy in the design and implementation of curriculum innovations.