In this work, support vector classification (SVC) algorithm was used to build structure-activity relationship (SAR) model of the 5-hydroxytryptamine type 3 (5-HT3) receptor antagonists with 26 compounds. In a benchmark test, SVC was compared with several techniques of machine learning currently used in the field. The prediction performance of the model was discussed on the basis of the leave-one-out cross-validation. The results show that the accuracy of prediction of SVC model was higher than those of back propagation artificial neural network (BP ANN), K-nearest neighbor (KNN) and Fisher methods.