The interface and nanoindentation mechanisms of alkanethiol self-assembled monolayers (SAMs) chemisorbed on a gold surface are investigated using molecular dynamics simulation. The mechanisms include the nanoindentation depths, the workpiece temperatures, the numbers of SAM layers, the length of united-atoms per chain, and the shapes of the indenters. The simulation results show that the disorder and the plastic mobility of SAM chains increased with increasing indentation depth. The relaxation force and the plastic energy almost linearly increased with increasing indentation depth. The disorder region after indentation at high temperature is larger than that at low temperature. The adhesive force shows a dependence on temperature during indentation. The potential energy decreases with increasing number of SAM layers. The structural morphologies of the SAMs were not affected at the third layers for SAM film with four layers. The maximum load quickly decreases for film with two SAM layers. The structures of the SAM can be easily tilted and bent when the united-atoms per chain length is long. The SAM atoms become more disorderly and the elastic recovery is smaller when the SAM length of the united-atoms per chain is long after indentation. (C) 2010 Elsevier Inc. All rights reserved.