The brainstem engages in various brain functions. However, we still lack a detailed understanding of its underlying functional organization. Therefore, in this study, we analyzed 222300 fMRI scans of 62 subjects acquired at the HCP-7 Tesla project. We applied the instantaneous parcellation analysis (ICP) method and determined a reliable, reproducible, and stable functional anatomy of the brainstem. The results reveal that stable multi-scale functional anatomy exists in the brainstem. The spatial rich functional anatomy enables neuroscientists to better characterize brainstem organization and understand its function and role in various brain disorders.