Abstract: As an emerging research field of brain science, multimodal data fusion analysis has attracted broader attention in the study of complex brain diseases such as Parkinson's disease (PD). However, current studies primarily lie with detecting the association among different modal data and reducing data attributes. The data mining method after fusion and the overall analysis framework are neglected. In this study, we propose a weighted random forest (WRF) model as the feature screening classifier. The interactions between genes and brain regions are detected as input multimodal fusion features by the correlation analysis method. We implement sample classification and optimal feature selection based on WRF, and construct a multimodal analysis framework for exploring the pathogenic factors of PD. The experimental results in Parkinson's Progression Markers Initiative (PPMI) database show that WRF performs better compared with some advanced methods, and the brain regions and genes related to PD are detected. The fusion of multi-modal data can improve the classification of PD patients and detect the pathogenic factors more comprehensively, which provides a novel perspective for the diagnosis and research of PD. We also show the great potential of WRF to perform the multimodal data fusion analysis of other brain diseases.