The nanocrystalline (NC) materials of several average grain sizes ranging from 11.61 to 31.32 nm were obtained by using the phase field crystal model (PFC), and the microscopic deformation mechanism of strengthening law for the uniaxial tensile deformation was discussed. Simulated results show that grain rotation and grain boundary (GB) migration are mainly responsible for the microscopic deformation. Since small grain size is favorable for grain rotation so that it can make the yield strength reduced; and the NC materials would show a reverse Hall-Petch effect. When the grain size is so small and the strain exceeds the yield point to about 4%, dislocation activities begin to occur. Mainly by the change of GB structure (disorganizing triple grain boundary junction and then promoting grain migration), the GB can play a finite contribution to deformation. With increasing grain size, grain rotation becomes difficult, and the grain serration and emission of dislocations are observed.