Sn-1,3 diacylglycerol (Sn-1,3 DAG) is widely applied as a functional lipid. Recently there has been escalating interest in understanding the acyl migration of sn-1,3 DAG that could bring about various physicochemical properties of the functional oils. In this study, 97.8% of sn-1,3 lauryl diacylglycerol (Sn-1,3 LDAG) and 98.3% of sn-1,3 palmityl diacylglycerol (Sn-1,3 PDAG) were synthesized by esterification and purified via crystallization using mixed solvent n-hexane: ethyl acetate = 92:8 (V/V) and n-hexane: ethyl acetate = 98:2 (V/V), respectively. Increasing temperature and system dispersion, enhanced the acyl migration rate (Km) of sn-1,3 DAGs and reduced its half-life (T1/2). As the acyl migration degrees (AMDs) of DAG increased, DAGs crystallization and melting were completed at a shorter temperature range and time while the crystal aggregation mode of DAGs shifted from disordered needle crystals to more organized Maltese cross-shape. Acyl-migrated LDAG forms β+β′ crystals, while acyl-migrated PDAG forms β+α crystals in 25 °C. The dynamics of acyl migration and crystallization of sn-1,3 DAGs can be applied to prepare high content sn-1,3 DAG products. The crystal morphology and polymorphism properties of sn-1,3 LDAG and sn-1,3 PDAG with different AMDs are beneficial to obtain functional sn-1,3 DAG customized products with desirable characteristics.