The oxygen vacancy in MnO2 is normally proved as the reactive site for the catalytic ozonation, and acquiring a highly reactive crystal facet with abundant oxygen vacancy by facet engineering is advisable for boosting the catalytic activity. In this study, three facet-engineered α-MnO2 was prepared and successfully utilized for catalytic ozonation toward an odorous CH3SH. The as-synthesized 310-MnO2 exhibited superior activity in catalytic ozonation of CH3SH than that of 110-MnO2 and 100-MnO2, which could achieve 100% removal efficiency for 70 ppm of CH3SH within 20 min. The results of XPS, Raman, H2-TPR, and DFT calculation all prove that the (310) facets possess a higher surface energy than other facets can feature the construction of oxygen vacancies, thus facilitating the adsorption and activate O3 into intermediate peroxide species (O2–/O22–) and reactive oxygen species (•O2–/1O2) for eliminating adjacent CH3SH. In situ diffuse reflectance infrared Fourier transform spectroscopy (in situ DRIFTS) revealed that the CH3SH molecular was chemisorbed on S atom to form CH3S–, which was further converted into intermediate CH3SO3– and finally oxidized into SO42– and CO32–/CO2 during the process. Attributed to the deep oxidation of CH3SH on 310-MnO2 via efficient cycling of active oxygen vacancies, the lifetime of 310-MnO2 can be extended to 2.5 h with limited loss of activity, while 110-MnO2 and 100-MnO2 were inactivated within 1 h. This study deepens the comprehension of facet-engineering in MnO2 and presents an efficient and portable catalyst to control odorous pollution.