Shave-off profiling with nano-beam SIMS achieves the highly precise depth profiling with nanometer-scaled depth resolution by utilizing FIB micro-machining process to provide depth profile. This method has its own features: absolute depth scale, pin point depth profiling and application to rough surface and/or hetero interface. However, the discussion of the sputtering mechanism in shave-off profiling is still insufficient because shave-off scan mode has distinctive position of the primary ion beam against the sample. In this study, the sputtering yield and the mixing effects within the primary ion dose amount of up to 1.0×10 16 ions/cm 2 under shave-off condition were investigated using molecular dynamics simulations. These results were compared with those of under conventional raster scan mode. In addition, the ejected region of sputtered atoms was investigated. As a result, it was proved that shave-off scan mode has high sputtering yield and low mixing effects. Moreover, the relationship between the sputtering phenomenon and the atomic displacement under shave-off scan mode was demonstrated.