Grain boundary plays an important role in determining a large number of material properties (e.g., strength, ductility, corrosion resistance, etc). In particular, a lot of attentions have been paid to special grain boundaries because of their special atomic structure and properties. By investigating the symmetry breaking during transformation and deformation, we propose a new method to produce special grain boundaries (GBs). The characteristic type of GBs generated is dictated by the broken symmetry during the process, which establishes a fundamental relationship between phase transformation and grain boundary engineering. Through a combination of phase transition graph analysis and phase field modeling, polycrystalline microstructures generated in Fe-based and Ti-based alloys and NiTi-bases shape memory alloys are investigated systematically and compared with experimental observations. The work provides new insight into engineering design of polycrystalline microstructure with mostly special grain boundaries through transformation and deformation.