The interface dynamics and nanoscratched mechanisms of alkanethiol self-assembled monolayers (SAM) chemisorbed on a gold surface are investigated using molecular dynamics simulation. The characteristic mechanisms mainly include the nanoscratched depths, the workpiece temperatures, the scratched speed, the SAM chain lengths, and the shapes of the indenters. The simulation results show that the disorder and the plastic mobility of SAM structures increased with increasing nanoscratched depth. The scratched forces, the potential energy, the friction force, and the friction coefficient increased with increasing scratched depth. The larger scratched depth required a larger force to overcome the resistance, which leads to the increases in the friction force. The variations of the scratched forces and the friction forces after scratching at various temperatures are very similar. An increase in the scratched force, friction force, and friction coefficient with increasing scratched speed is observed. The scratched shape after scratching is clearer for a longer SAM chain. The SAM structures are easily tilted and bent when the chain length is longer. The reaction forces after scratching using a spherical indenter are higher than those after scratching using a Vickers indenter.