By density functional theory (DFT), we report a detailed mechanistic study on the synthesis of methylacrolein (MAL) by a mild Mannich reaction of formaldehyde (FA) and propionaldehyde (PA) catalyzed by sec-amine short-chain aliphatic acid ionic liquids (ILs). ILs exhibit excellent catalytic activity and create mild reaction conditions (45 °C) by dramatically decreasing the reaction energy barrier (24.43 kcal mol −1 ) in the decomposition step of Mannich bases (MBs) comapred to without ILs. Three key intermediates observed by DFT calcutations were identified by electron spray ionization mass spectrometry (ESI-MS) analysis. We systematically investigated the catalytic effect of ILs with different sec-amines (HNR 2 , R = CH 3 , C 2 H 5 , etc.) on the activation energy and different short-chain aliphatic acids (RCOOH, R= H, CH 3 et al.) on the decomposition step of MBs. This work is intended to provide a thorough explanation of the synthesis mechanism of the mild Mannich reaction of MAL catalyzed by ILs from the theoretical aspect, which may give a favorable guidance for the practical application.