The two-mode phase field crystal (PFC) method is used to calculate the phase diagram. And in this paper it is used to simulate the effects of predeformation degree and isothermal temperature on the hexagonal grain boundary evolution and on the hexagonal/square phase transition. Results show that when there is no predeformation in the initial phase, the grain boundary defect causes the pre-melting around the melting point; predeformation increases and the interaction between deformation and defects induces the pre-melting around the melting point; and the predeformation further increases, deformation induces liquid phase and square phase simultaneously at the distortion place. The bigger the predeformation and the closer to melting point the maintained temperature, the more obvious the growth of liquid phase is; on the contrary, the square phase grows obviously. The distortion energy is released with time and the phase of grain finally becomes square phase. It can be concluded that keeping the hexagonal phase isothermal near the melting temperature, the liquid phase appears at the grain boundary or at the other defects because the predeformation leads to the increase of atom activity, thus increasing atom disorder degree. Then with the release of distortion energy, the grain phase finally transforms into an equilibrium square phase. In this way the hexagonal/square transition time is extended.