The arrival of the era of big data has brought new ideas to solve problems for all walks of life. Medical clinical data is collected and stored in the medical field by utilizing the medical big data platform. Based on medical information big data, new ideas and methods for the differential diagnosis of hypo-MDS and AA are studied. The basic information, peripheral blood classification counts, peripheral blood cell morphology, bone marrow cell morphology, and other information were collected from patients diagnosed with hypo-MDS and AA diagnosed in the first diagnosis. First, statistical analysis was performed. Then, the logistic regression model, decision tree model, BP neural network model, and support vector machine (SVM) model of hypo-MDS and AA were established. The sensitivity, specificity, Youden index, positive likelihood ratio (+LR), negative likelihood ratio (−LR), area under curve (AUC), accuracy, Kappa value, positive predictive value (+PV), negative predictive value (−PV) of the four model training set and test set were compared, respectively. Finally, with the support of medical big data, using logistic regression, decision tree, BP neural network, and SVM four classification algorithms, the decision tree algorithm is optimal for the classification of hypo-MDS and AA and analyzes the characteristics of the optimal model misjudgment data.