The investigation of lightning impulse (LI) breakdown characteristics in long oil gaps with insulating liquids is of utmost importance for the design of high-voltage, large-capacity transformers. This study focuses on analyzing the negative LI breakdown characteristics of two types of insulating oils, namely high viscosity natural ester soybean oil (SO) and low viscosity modified natural ester palm fatty acid ester (PFAE), under long oil gap conditions. The research includes testing and analyzing the voltage and current waveforms, LI breakdown voltage, and streamer discharge development speed of these liquids across oil gaps ranging from 25 mm to 105 mm. The findings demonstrate that the breakdown voltage of both insulating oils tends to increase as the oil gap distance widens. At a 25 mm gap, the average breakdown voltage of PFAE is not significantly different from that of SO. However, at a 105 mm gap, the average breakdown voltage of PFAE surpasses that of SO by 46.29%. Weibull distribution analysis is applied to the LI breakdown voltage data of the two insulating liquids, resulting in empirical formulas for breakdown voltage as a function of oil gap width at failure probabilities of 1%, 50%, and 90%. The discharge development rate of PFAE is lower than that of SO, especially in the oil gap of 105 mm. With the increase of the oil gap, the streamer development rate of the two insulating oils showed a trend of increasing. Using density functional theory based on first principles, the study investigates changes and discrepancies in parameters such as ionization potential, electron affinity, softness, excitation energy, and molecular surface electrostatic potential of the two insulating liquids with varying electric field strengths. The atomic and molecular scale analysis reveals the primary factors contributing to the contrasting macroscopic lightning shock breakdown characteristics of SO and PFAE. The comprehensive combination of experimental and simulation results suggests that PFAE exhibits greater potential for implementation in high-voltage, large-capacity transformers compared to SO. This study aims to bridge the gap in knowledge regarding the LI breakdown characteristics of different natural esters in long oil gaps. The experimental and theoretical findings presented in this paper provide a foundation for the practical application of natural esters and modified natural esters in high-voltage and large-capacity transformers.