Modified natural ester (MNE) has significant potential for application in transformers as an environmentally friendly and renewable energy source. In comparison to natural esters, MNE offers notable advantages in terms of viscosity and power frequency breakdown voltage. However, the lightning impulse breakdown characteristics of MNE and the atomic-scale microscopic mechanisms related to its discharge characteristics remain unclear. Understanding the lightning impulse breakdown characteristics of MNE is crucial for ensuring the safe operation of transformers. In this paper, the density functional theory is used to calculate the change law of the microscopic parameters related to the discharge characteristics of MNE under the electric field under the action of electric field, so as to theoretically evaluate the lightning impulse discharge behavior of MNE. The results reveal that the electronic and geometric structures of MNE molecules are influenced by electric fields, which is the primary factor contributing to the variations in microscopic parameters under different electric field strengths. As the electric field intensity increases, the dipole moment of MNE tends to increase, while the ionization potential and excitation energy of MNE tend to decrease. The decrease of ionization potential, excitation energy and energy gap of MNE molecules is about 6.61%–68.01%, 4.34%–47.66% and 2.01%–69.23%. By comparing the calculated results of mineral oil, natural ester, and MNE microparameters, it can be inferred that the lightning impulse breakdown behavior of MNE is similar to that of natural ester and lightning impulse breakdown voltage of MNE is higher than that of natural ester but still lower than that of mineral oil. The average negative polarity lightning impulse voltages of MNE, natural ester and mineral oil in the 85 mm oil gap are about 245 kV, 199 kV and 304 kV, respectively. The test results confirmed the simulation conclusions. This study provides robust theoretical support for understanding the lightning impulse breakdown characteristics of MNE and ensuring its safe operation in transformers.