Palm olein (POL) was modified by enzymatic interesterification with different degrees of acyl migration in a solvent-free packed bed reactor. The fatty acid and acylglycerol composition, isomer content, thermodynamic behavior, and relationship between crystal polymorphism, solid fat content (SFC), crystal microstructure, and texture before and after modification were studied. We found that the increase in sn-2 saturation interesterification was not only due to the generated tripalmitin (PPP) but also caused by acyl migration, and the SFC profiles were changed accordingly. The emergence of high melting point acylglycerols was an important factor accelerating the crystallization rate, further shortening the crystallization induction time, leading to the formation of large crystal spherulites, thereby reducing the hardness. The transformation from the β' to the β form occurred during post-hardening during storage. The isomer content also affected the physicochemical properties of the modified POL.