Although sustainable lubricants exhibit excellent performance and eco-friendly characteristics, further research is still needed to fully understand how they affect environmental systems, particularly after mechanical servicing. Herein, five ester oils with distinct structures were applied to explore their physicochemical property, lubricating performance, and phytotoxicity in order to make a profound study on the relevant structure–activity relationship of ester lubricants. Trimethylolpropane trioleate (TMPTO) and pentaerythritol oleate (PETO) were found to have the best viscosity–temperature characteristics. The friction coefficients of PETO and TMPTO are relatively small, and the order of wear volume is pentaerythritol tetraisooctanoate (PIS) > diisooctyl sebacate (DOS) > trioctyl trimellitate (TOTM) > TMPTO > PETO. Following, for different plants, the toxicity magnitude order becomes TOTM < PETO < TMPTO < DOS < PIS (wheat, germination, stem length, and root length) and TOTM < TMPTO < PETO < DOS < PIS (Pak choi, germination, and stem length). By the biochemical level, wheat seedlings displayed an inhibition of photosynthetic pigments. Meanwhile, antioxidant enzyme activities superoxide dismutase (SOD), CAT (hydrogen peroxide enzyme), peroxidase (POD), and ascorbate peroxidase (APX) exhibited a decreasing trend. This work can provide theoretical guidance for the development of environmentally friendly and high-performance lubricants.Studying the structure−activity relationship between structure and performance provides a foundation for the design of sustainable high-performance lubricants.