Miniaturization of electronic devices down to the nanoscale needs corresponding processing technologies with precision at the atomic layer level. The plasma atomic layer etching (ALE) technique is playing an active role in this demand. However, theoretical research on the ALE mechanism is a great challenge. We propose a method of spontaneously searching adsorption sites (SSASs) to understand what surface chemistry occurs in the ALE processing of MoS2 treated by the remote oxygen plasma. The SSAS results are in good agreement with experimental observations. Chemical adsorption of O atoms occurs only in the topmost layer of the MoS2 surface. The MoS2 surface has four different adsorption sites with different probabilities of binding an O atom, denoted by 0Sbb, 0Sbbc, 2Sbb, and 3Sbb configurations, which have zero, zero, two, and three S-Mo bonds broken by the introduced O atom, respectively. Four adsorption sites of the MoS2 surface play different roles in the surface oxidation in the remote oxygen plasma.