Siloxane working fluid has good environmental performance and thermodynamic performance, widely used in high temperature heat source ORC system. During the filling process of working fluid and operation in ORC system operation, air may leak into the system. The reaction of siloxane working fluid with oxygen in high temperature environment will produce abrasive silica, which will cause serious damage to the system. The oxidative decomposition mechanism of hexamethyldisiloxane (MM) was analyzed by density functional theory (DFT) and ReaxFF molecular dynamic simulation. It is found that the initial reactions of MM oxidation decomposition can be divided into two categories. The first type is the thermal decomposition of MM itself. The second one is the collision reaction between MM molecule and O2 molecule. Comparing the two kinds of chemical reaction barriers, MM is more likely to react with O2. Pathways 2–3 involving the collision between O2 molecule and Si atom are the optimal pathway of initial reaction kinetics, and its reaction energy barrier is 204.1 kJ/mol. It was observed from ReaxFF MD simulations that the main products of MM oxidative decomposition were CH4, CH2O, CO, CO2, SiO and amorphous silica. In the process of oxidative decomposition, small free radicals such as CH3, O, H, OH played a very important role in the oxidative decomposition of working fluids, which greatly promoted the decomposition of working fluids and the formation of main products.