Comonomer defects can induce semicrystalline polymers to form unique crystalline structures (e.g., defect crystals), which can greatly influence the materials' physical properties. However, the formation mechanism and structural evolution of defect polymer crystals are not yet well understood. Herein, we chose the poly(l-lactic acid) (PLA) containing glycolic acid (GA) units as the model defect-containing polymer and investigated its crystallization structure and phase transition. The presence of GA units reduces the crystallizability of PLA and leads to the formation of unique defect crystals with enlarged unit cell size. The formation of defect crystals is favored at a low crystallization temperature or high content of GA units due to the inclusion of more comonomer defects. The defect crystals are metastable and undergo structural ordering to form thermally stable α-crystals upon heating and high-temperature annealing, as governed by the exclusion of comonomer defects. This work sheds light on the crystallization and phase transition of defect-containing polymers.