In this work, the isomer mixture of 4,4′-diphenylmethane diisocyanate (MDI) and 2,4′-MDI was separated and purified by dynamic falling film melt crystallization, and 99.3% purity and 50.8% yield of 4,4′-MDI could be obtained under optimized conditions. The separation mechanism was simulated by density functional theory (DFT) and molecular dynamics (MD) simulation. Results showed that compared with 2,4′-MDI, 4,4′-MDI molecules could form a more stable and symmetrical crystal structure due to their stronger charge density symmetry and electrostatic potential energy. Furthermore, the separation phenomenon and the formation of the crystal structure were observed according to the radial distribution function (RDF) and orientation correlation function obtained from MD simulation. Finally, the attachment energy (AE) model was used to observe and compare different crystal surfaces; it was proposed that the aggregation of 4,4′-MDI was attributed to the polar attraction between isocyanate groups according to the results of the orientation correlation function. It was also observed that compared with 2,4′-MDI, 4,4′-MDI molecules on the (110) crystal surface were easier to form crystal structures.