Multidrug-resistant tuberculosis (MDR-TB) has become a major public health problem. We tried to apply the classification tree model in building and evaluating a risk prediction model for MDR-TB. In this case-control study, 74 newly diagnosed MDR-TB patients served as the case group, and 95 patients without TB from the same medical institution served as the control group. The classification tree model was built using Chi-square Automatic Interaction Detectormethod and evaluated by income diagram, index map, risk statistic, and the area under receiver operating characteristic (ROC) curve. Four explanatory variables (history of exposure to TB patients, family with financial difficulties, history of other chronic respiratory diseases, and history of smoking) were included in the prediction model. The risk statistic of misclassification probability of the model was 0.160, and the area under ROC curve was 0.838 (P < 0.01). These suggest that the classification tree model works well for predicting MDR-TB. Classification tree model can not only predict the risk of MDR-TB effectively but also can reveal the interactions among variables.