Side substitution is an effective method for the chemical modification and functionalization of linear polyesters. The presence of side groups can have a profound effect on the crystalline structure and phase transition of semicrystalline polyesters. Herein, we synthesized the long-spaced polyesters with -OH and -CH3 side groups and various methylene segment lengths and studied the effects of the side groups on the crystal polymorph and phase transition of substituted polyesters. The substituted polyesters grow in the thermally stable phase (form I) at a higher temperature. However, the polyesters crystallize in a metastable hexagonal phase (form II) with trans chain conformation at a lower temperature. The metastable form II transforms into the more stable form I during long-time annealing or upon heating; this phase transition is accompanied by chain tilting and crystal lamellar thickening. This study has elucidated the critical role of side groups in the polymorphic crystallization and phase transition of linear polyesters.