High-melting point 1,3-diacylglycerols not only provide health benefits, but are also suitable for manufacture of foods containing various specialty fats. It is difficult to prepare such high-melting point diacylglycerols, as the activities of specific enzymes will severely reduce at their melting points. In the present study, a combined technique was developed to prepare 1,3-dipalmitoylglycerol (1,3-DPG) and 1,3-distearoylglycerol (1,3-DSG) using selective esterification, molecular distillation, and solvent fractionation. Lipozyme TL IM was suitable for use as the optimal enzyme to maintain relatively high activity levels at esterification temperatures of 73–75 °C. 1,3-DAG/(DAG + TAG) was selected as the most important index to monitor the esterification and to evaluate the synthesized fats. The obtained 1,3-DPG and 1,3-DSG showed high purities, at more than 83%, and possessed hard attributes at room temperature. Both 1,3-DPG and 1,3-DSG exhibited fat crystals with β′ and β crystals. Needle-like and rod-like crystals were observed at 5–25 °C for 1,3-DPG, and closely packed feather-like crystals were found at 5–20 °C for 1,3-DSG, indicating their multiple abilities in modifying the crystallization stabilization of the fat matrix during food processing.