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The oxidation mechanism of atomically thin molybdenum disulfide (MoS2) plays a critical role in its nanoelectronics, optoelectronics, and catalytic applications, where devices often operate in an elevated thermal environment. In this study, we systematically investigate the oxidation of mono- and few-layer MoS2 flakes in the air at temperatures ranging from 23 °C to 525 °C and relative humidities of 10%–60% by using atomic force microscopy (AFM), Raman spectroscopy and x-ray photoelectron spectroscopy. Our study reveals the formation of a uniform nanometer-thick physical adsorption layer on the surface of MoS2, which is attributed to the adsorption of ambient moisture. This physical adsorption layer acts as a thermal shield of the underlying MoS2 lattice to enhance its thermal stability and can be effectively removed by an AFM tip scanning in contact mode or annealing at 400 °C. Our study shows that high-temperature thermal annealing and AFM tip-based cleaning result in chemical adsorption on sulfur vacancies in MoS2, leading to p-type doping. Our study highlights the importance of humidity control in ensuring reliable and optimal performance for MoS2-based electronic and electrochemical devices and provides crucial insights into the surface engineering of MoS2, which are relevant to the study of other two-dimensional transition metal dichalcogenide materials and their applications.