Migration is an important issue for the security in food packaging. In this work, the migration mechanism of plasticizer in G50 starch ester nanocomposites and accompanying multi-scale structural changes were probed with immersion. Mathematical model manifested that the migration mechanism of plasticizer obeyed the first-order kinetic model, and the migration of plasticizer followed the Fick’s second law in the short-term migration. In the meantime, the interactions between G50 starch ester and nanoparticles (OMMT) were enhanced by the migration, which was in favor of reducing the migration and bringing about a smaller diffusion coefficient (D) in the long-term migration compared with short-term ones. Meanwhile, the strengthened interactions conduced to accelerating the motion of starch ester, and altering the dispersion of OMMT, which resulted in the transformation from intercalation to exfoliation with the vanish of small inter-planar spaces for crystals. Simultaneously, these conversions increased the electron density contrast in amorphous and ordered regions, showing an increment of the roughness with wrinkles in the cross-sections. Based on above researches, the migration behaviors of plasticizer in starch ester nanocomposites were well expounded, while it is still necessary to explore new ways to inhibiting the migration of plasticizer in food packaging materials.