BACKGROUNDThe relative low stability, reusability and activity of enzymes made the industrial production of vitamin E succinate (VES) can only be performed with complex processes and high cost using chemical methods. To address these issues, in the present study, an ionic liquids (ILs) modification strategy was developed to improve the activity and stability of lipases in VES synthesis.RESULTSThe results showed that the [1‐butyl‐3‐methyl imidazole] [N‐acetyl‐l‐proline] ILs modified Candida rugosa lipase (CRL) has the highest modification degree (48.28%), activity (774 U g−1), thermostability and solvent tolerance in three selected modifiers. Additionally, after reaction condition optimization, the highest yield of VES can be improved to 95.18% at 45 °C for 15 h, which was significantly improved compared to some previous studies.CONCLUSIONIn the present study, a high‐efficiency VES synthesis strategy was successfully developed via modification of lipase. Moreover, the mechanism by which ILs modification can enhance the activity and stability of lipase was investigated via both experimental and computational‐aided methods. Molecular dynamics simulation suggested that ILs modification changed the geometry of Phe344 from flat to upright, which significantly reshaped and enhanced the size of substrate binding pocket of CRL. It is also agreement with our circular dichroism and fluorescence spectroscopy results, which suggested that the modification changed the secondary structure of CRL to a certain extent. The larger pocket also endowed the suitable binding pose of succinate, which made the hydrogen bonds between succinate and active site Ser209 become stronger, and thus improving the yield of VES. © 2023 Society of Chemical Industry.