We report both cracking and self-healing in crystals occurring during a thermal phase transition, followed by a topochemical polymerization. A squaramide-based monomer was designed where the azide and alkyne units of adjacent molecules are positioned favorably for a topochemical click reaction. The monomer undergoes spontaneous single-crystal-to-single-crystal (SCSC) polymerization at room temperature via regiospecific 1,3-dipolar cycloaddition, yielding the corresponding triazole-linked polymer in a few days. When heated at 60 °C, the polymerization completes in a SCSC manner in 24 h. Upon continuous heating from room temperature to 110 °C, the monomer crystals develop multiple cracks, and they self-heal immediately. The cracking occurs due to a thermal phase transition, as evidenced by differential scanning calorimetry (DSC). The cracks heal either upon further heating or upon cooling of the crystals due to the topochemical polymerization or reversal of the phase transition, respectively. Increasing the heating rate leads to the formation of longer and wider cracks, which also heal instantaneously. The self-healed crystals retained their integrity and the crystal structure of the self-healed crystals was analyzed by single-crystal X-ray diffraction. The quality of the self-healed crystals and their diffraction ability conform to those of the completely reacted crystals at room temperature or at 60 °C without developing cracks. This work demonstrates a novel mechanism for self-healing of molecular crystals that could expand the horizon of these materials for a plethora of applications.