Understanding the impulse discharge behaviour of natural ester (NE) is crucial for its safe application in high‐voltage transformers. The ionisation potential (IP) of triglycerides plays a significant role in the process of molecular ionisation during impulse discharge for NE. The correlation coefficients between molecular size, frontier orbital, electrostatic potential, polarity, and IP were analysed. And the quantitative microstructure‐IP model for triglycerides were built, which revealed that IP is strongly related to the highest occupied molecular orbital (HOMO) energy EHM, as well as the average value of positive electrostatic potential Vp(+), the average value of negative electrostatic potential Vp(−), and the surface area of negative electrostatic potential S(−). The HOMO and negative electrostatic potentials of saturated triglycerides are predominantly linked to the carbonyl O atoms. Conversely, in unsaturated triglycerides, the influence of C=C double bonds on HOMO and negative electrostatic potentials is more pronounced. Therefore, the IP of unsaturated NE with C=C bonds is lower than that of saturated NE, rendering it more susceptible to ionisation under a strong electric field which is unfavourable for impulse breakdown voltage. The structure‐property correlation analysis is valuable for understanding ionisation mechanism during the impulse discharge breakdown of NE at the microscopic level.