The microstructure of lipids significantly affects the three-dimensional network, ultimately determining their physical properties. Due to the unique physical properties of diacylglycerol (DAG), it can be effectively used as a functional substitute for traditional oil in plastic fats. This study explored the microstructure and physicochemical properties of high-purity sn-1,3 lauryl diacylglycerol (LDAG), palmityl diacylglycerol (PDAG), and their acyl migration equilibrium products (ME-DAG, sn-1,3 DAG: sn-1,2 DAG = 65:35) under different cooling rates. As the cooling rate increased, the hydrogen bond force and order degree of DAGs also rose. Sn-1,3 LDAG exhibited a larger lattice space, thicker nanoplatelet structure, and larger crystals than sn-1,3 PDAG at the micro-scale. The increasing cooling rate resulted in the transformation of β