This study aims to classify and differentiate mucinous and serous cystic neoplasms of the pancreas using a multi-source feature classification model based on deep learning for preoperative auxiliary diagnosis. Deep learning features and radiomics features were extracted from segmented images using deep learning and radiomics technology, respectively. Clinical features were also evaluated and quantified. LASSO (least absolute shrinkage and selection operator) and cross-validation methods were applied to screen the features, and two multi-source feature models were constructed: the radiomics combined with deep learning (RAD_DL) model and the clinical feature combined with RAD_DL (Clinical_RAD_DL) model. Traditional radiomics (RAD) and deep learning (DL) models were used as controls. SVM (support vector machine), ADAboost (adaptive boosting), Random Forest, and Logistic were selected for classification. The Clinical_RAD_DL feature model shows the best classification performance, with the accuracy of 0.923 1, recall rate of 0.882 4, precision of 0.882 0, F1-score of 0.882 2, and AUC value of 0.912 6. The experimental results indicate that the multi-source feature classification model based on deep learning has good performance in classifying pancreatic serous cystic neoplasms and pancreatic mucinous cystic neoplasms, and can assist clinical accurate diagnosis and treatment.