The molecular structure of the fatty acid ester has a significant influence on the properties of the ester-based drilling fluid. Based on the study on the number of ester groups, saturation, molecular configuration, molecular size and intermolecular force of the molecules of fatty acid esters, this paper selected 6 kinds of saturated fatty acid esters as the research mediums. The viscosities and densities of these mediums at different temperatures were tested and the mechanism that influences the viscosities and densities was analyzed, it was demonstrated that the viscosities of the mediums under low temperatures mainly depend on the length of the fatty alcohol molecular chain; whereas the densities of mediums mainly rely on the molecular size, which have no relationship with the molecular symmetry, α-hydrogen activation and intermolecular force.