Based on the three-dimensional structures of the compounds, the structures of 48 ester compounds were expressed parametrically. Through multiple linear regression and partial least-squares regression, the relationship models between ester compound structures and aquatic toxicity log(1/IGC50) were established. The correlation coefficients (R2) of the models were 0.9974 and 0.9940, and the standard deviations (SD) were 0.0469 and 0.0646, respectively. The stability of the models was evaluated by the leave-one-out internal cross-test. The correlation coefficients (RCV2) of the models of interactive tests were 0.9939 and 0.8952, and the standard deviation (SDCV) was 0.0715 and 0.0925, respectively. The external samples were used to test the predictive ability of the models, and the correlation coefficients (Rtest2) of the external predictions were 0.9955 and 0.9955, and the standard deviations (SDtest) were 0.0720 and 0.0716, respectively. The molecular structure descriptors could successfully represent the structural characteristics of the compounds, and the built models had good fitting effects, strong stability and high prediction accuracy. The present study has a good reference value for the study of the structure-toxicity relationship of toxic compounds in the environment.