Chemical sputtering on a graphite (0 0 0 1) surface due to hydrogen atom bombardment was investigated by a molecular dynamics simulation. To understand the temperature dependence of the sputtering yield of CH x and C 2 H x , two thermostat methods used to control material temperature, the Langevin and Berendsen thermostats, were compared. The simulated sputtering yield of CH 4 with a peak at 600 K under the Langevin thermostat agreed with experimental observations. The present simulation showed that the sputtering yield depends on the thermal relaxation time, which is the time required for the temperature to reduce and is the second key parameter for both thermostat methods. In addition, it was demonstrated that the Berendsen thermostat, which controls temperature globally, provides larger sputtering yields of CH x and C 2 H y than the Langevin thermostat, which controls temperature locally.