In this study, high-energy shot peening (HESP) was used to treat the surface of a medical titanium alloy, and the microstructure evolution and micromechanical properties during the treatment process were studied using scanning electron microscopy (SEM), atomic force microscopy (AFM), transmission electron microscopy (TEM), and microindentation. Research has shown that after HESP treatment, a gradient structure is formed on the surface of the material. With increasing impact time, the surface roughness of the material first increases, then decreases, and then gradually stabilizes. TEM analysis shows that nanocrystals are formed at the surface of the material after HESP treatment. Microindentation analysis reveals that the elastic modulus of the strengthened sample decreases as the processing time increases, with a minimum value of approximately 59.026 GPa appearing at the surface position after 60 min of treatment, a decrease of 15.78% compared to that of the untreated sample. Moreover, with increasing shot peening time, the yield strength and strain hardening index gradually increase.