A comprehensive understanding on interaction among grains, boundaries, strain and dislocations are beneficial for microstructure optimization and properties enhancement. A two-mode phase field crystal (PFC) method is employed to focus on hexagonal to square phases transformation. Hexagonal phases with a misorientation of 6° and tilt angle of 0 °, 15°, 30°, and 45° are checked. The hexagonal grains grow up, coalesce and form coherent grain boundaries with dislocation sets in two orientations. Square phases nucleate on these dislocation sets and their orientations are determined by these dislocation sets. These square grains of each case have two variants, which the misorientations are 30°, 30°, 10°, and 5° when tilt angles are 0 °, 15°, 30°, and 45°. Square grains of different orientation grow and ripen in different pace, the grains that locate on preferential orientation will dominate. Dislocation sets are generated to relieve strain concentration that rises from grain growth with coherent boundaries.