Midbrain atrophy is strongly associated with progressive supranuclear palsy (PSP) disease severity. Preclinical evidence suggests that midbrain-based Magnetic Resonance Parkinsonism Index (MRPI) measurements are reliable and sensitive morphometric biomarkers for PSP diagnosis. The study explored the longitudinal changes of MRPI measurements in PSP patients. Midbrain-based morphometric measurements and the corresponding annual percentage changes were measured and further used to evaluate the associations with disease progression. Compared with healthy controls, baseline quantitative analyses in patients with PSP revealed significant differences in all morphometric measurements expect pons. Baseline comprehensive measurements were significantly associated with baseline PSP rating scale score (P < 0.05). Our study demonstrates that midbrain-based MRPI measurements holds promise for monitoring PSP disease progression.