Lateral heterostructures of 2D materials have several interesting properties and potential applications, and they are usually fabricated by chemical vapor deposition. However, it still remains a great challenge to fabricate 2D lateral heterostructures with well-controlled patterns and sharp interfaces. Herein, we found that the 2D α-Mo2C crystal, a recently emerging 2D superconductor, experiences a phase transition from the α phase to β phase on electron beam irradiation in a transmission electron microscope because of the migration of carbon atoms among the molybdenum octahedrons. Combined with first-principles calculations, the carbon atom migration paths and the corresponding energy barriers were discussed. Utilizing this unique phase transition property of 2D α-Mo2C crystal, we demonstrated the precise in situ construction of the lateral heterostructure of 2D superconducting α/β Mo2C with a well-controlled pattern and sharp interface using advanced aberration-corrected scanning transmission electron microscopy.