Feature representation is the crucial factor for the magnetic resonance imaging (MRI) based computer-aided diagnosis (CAD) of Parkinson’s disease (PD). Deep polynomial network (DPN) is a novel supervised deep learning algorithm, which has excellent feature representation for small dataset. In this work, a stacked DPN (SDPN) based ensemble learning framework is proposed for diagnosis of PD, which can improve diagnostic accuracy for small dataset. In the proposed framework, SDPN was performed on each subset of extracted features from MRI images to generate new feature representation. The support vector machine (SVM) was then adopted to perform classification task on each subset. The ensemble learning algorithm was then performed on all the SVM classifiers to generate the final diagnosis for PD. The experimental results on the Parkinson’s Progression Markers Initiative dataset (PPMI) showed that the proposed algorithm achieved the classification accuracy, sensitivity and specificity of 90.15%, 85.48% and 93.27%, respectively, with the brain network features, and it also got the classification accuracy of 87.18%, sensitivity of 86.90% and specificity of 87.27% on the multi-view features extracted from different brain regions. Moreover, the proposed algorithm outperformed other algorithms on the MRI dataset from PPMI. It suggests that the proposed SDPN-based ensemble learning framework has the feasibility and effectiveness for the CAD of PD.