The molecular structure of lubricating oil affects its lubrication properties, catalytic and hydrolytic stability, and anti-wear properties. Based on the idea of material genomics, researchers are trying to find the correlation between structural characteristics and functional performances of lubricating oil, but the correlation can only explore the influence weight of structural parameters on performance, it is also very important to research the influence mechanism. In this study, through quantum mechanics/molecular mechanics calculations, (i) the spatial configurations of four typical ester lubricants with different chain length structures were studied, (ii) effects of active functional groups and charge distribution on the properties of the ester lubricants were discussed, and (iii) electronic transition and molecular orbital contributions were compared. The calculated results are expected to provide considerable support for theoretical research on the anti-wear and anti-oxidation mechanisms of ester lubricants and assist the rapid design, development and application of lubricating materials.