Natural gas, which is mainly composed of methane, plays an important role in energy consumption. Nevertheless, natural gas leakage induced by damage of moving parts seriously affects the ecological environment and social security. It is an effective strategy to coat amorphous carbon (a-C) film on moving parts for this issue. In order to supplement the knowledge about frictional mechanism of a-C film in methane atmosphere, the roles of passivation and graphitization were explored by means of deposition target currents and thermal annealing. The results indicated that carbon target currents and thermal annealing were significant to the structures and tribological performances of a-C films under methane. It was also obtained that graphitization induced by shearing greatly enhanced the wear resistance of a-C film and the passivation of carbon dangling bonds reduced friction coefficients of a-C films in methane atmosphere. This study on the mechanism of friction properties of a-C films under methane provides guidance for the preparation of low friction and wear resistance films in methane atmosphere.