Sliding friction at nanometer scale has become an important factor in the miniaturization of moving components in which the empirical laws of friction do not always hold. This paper carries out large-scale parallel molecular dynamics simulation on sliding friction at atomic scale to uncover the special physical essence. The simulation result shows that both of the elastic deformation normal to the sliding direction at the local area and the edge dislocation are generated in the bulk materials. The successive generation and fracture of the molecular junction between a friction pair ought to be the key reason for the variation of friction force. Furthermore, end failure is observed under both larger or smaller sliding velocity although it does not increase linearly by increasing velocity, that is to say, the end failure decreased if the velocity was larger than some critical value. Different kinds of materials transfer mode is observed in the friction process under different sliding velocity because of the different cross-section of the interaction surfaces. The stick-slip feature of this nanoscale sliding friction with zero separation is different from what was observed at a microscale and should be the integral effect of different control mechanism and the corresponding dynamic behavior.