Ni-based superalloys with excellent high temperature strength have been used in advanced thermal power plants. It was found that grain boundary cracking is caused in the alloy under creep-fatigue loading due to the degradation of the crystallinity of grain boundaries and the grain boundary cracking degrades the lifetime of the alloy drastically. In order to clarify the mechanism of intergranular cracking, in this research, static and dynamic strains were applied to a bicrystal structure of the alloy perpendicularly to the grain boundary using molecular dynamics analysis. In addition, the effect of the accumulation of vacancies in the area with high-density of dislocations on the strength of the bicrystal structure was analysed. It was found that the fracture mode of the bicrystal structure changed from ductile transgranular fracture to brittle intergranular one as strong functions of the combination of Schmid factor of the two grains and the density of defects around the grain boundary. The local heavy plastic deformation occurred around the grain boundary with large difference in Schmid factor between nearby grains and the diffusion of the newly grown dislocations and vacancies was suppressed by the large strain field due to the large mismatch of the crystallographic orientation between the grains. The accumulation of vacancies accelerated the local plastic deformation around the grain boundary. Therefore, the mechanism of the acceleration of intergranular cracking under creep-fatigue loading was successfully clarified by MD analysis.