Grain boundary (GB) research is always the most fundamental and active study field in interface science. Grain boundary premelting (GBPM) is induced as a consequence of local inner strain around defects in material at high temperature. When GB premelting is under an external stress, it is referred to as stress induced GBPM (SIGBPM). Owing to the fact that the width of a GB usually is a few atoms thick, it is difficult to observe the GBPM directly in experiment, thus the development of computational simulation experiment can make up for the shortcomings in experiment. For this reason, a new method which is named phase field crystal (PFC) model based on density functional theory is proposed. Because the method can be used to simulate the evolution of macroscopic structure of polycrystalline material on a diffusive time and atomic scale, therefore, PFC has a great advantage in simulating the evolution of microstructure. In this paper, PFC method is used to investigate the annihilation process of dislocation pairs of premelted grain boundary under strain at high temperature. Simulated results show that the essence of separation process of sub-GB (SGB) from original GB is that sub-grain structures are generated. The SGB migration is the process of the new grain swallowing up the old one. The annihilation process of GBPM under applied strain at high temperature can be divided into two stage features. The first stage is the stage of system energy increasing, which is corresponding to the process of SGB migration, dislocation gliding; the second stage is the energy decreasing, which corresponds to the interaction of SGBs and annihilation of dislocations, while the speed of annihilation in this process is slow and the peak of energy curve is wide and smooth. According to the changing process of the atomic density distribution projected along the directions of x and y axis with strain increasing, we can reveal that the nature of annihilation of double dislocation pairs at high temperature is the process of two-step annihilations, of which the detailed process is not easy to observe at low temperature due to its fast annihilating speed of dislocation pairs.