The lightning impulse breakdown properties of natural esters are very important for their further applications. This paper focuses on the discharge mechanism investigation of a natural ester insulating liquid under a lightning impulse electric field. Based on density functional theory (DFT), the configuration, electron structure, ionization and electron affinity process, excitation process and molecular orbital of natural ester molecules were calculated under different electric field strengths. A correlation mechanism between the micro-physical parameters of ester insulating liquid molecules and discharge was proposed. The molecular electrostatic potential was used to predict the active point of discharge. The results show that the molecular structure of triglycerides shows yield behaviour under electric field action. The electrons are redistributed in the direction of the source of the electric field. Among the four triglycerides, the ionization and electron affinity process, excitation process and molecular orbital of glycerol tripalmitate were least affected by the electric field. The microscopic properties of other triglycerides were significantly affected by the electric field. According to the electrostatic potential (ESP) result of natural ester molecules, it can be predicted in the experiment that the surface of H atoms of the triglyceride ester group easily forms electron traps to bind electrons, while the surface of an O atom at the ester of a triglyceride undergoes electron collisions resulting in an electrical discharge. The proportion of palmitic acid in natural esters could be increased or pure glycerol tripalmitate could be used as an insulating oil to solve the problem of the low lightning impulse breakdown voltage of natural esters.