Introduction: Brain diseases, particularly the classification of gliomas and brain metastases and the prediction of HT in strokes, pose significant challenges in healthcare. Existing methods, relying predominantly on clinical data or imaging-based techniques such as radiomics, often fall short in achieving satisfactory classification accuracy. These methods fail to adequately capture the nuanced features crucial for accurate diagnosis, often hindered by noise and the inability to integrate information across various scales. Methods: We propose a novel approach that mask attention mechanisms with multi-scale feature fusion for Multimodal brain disease classification tasks, termed Results: Our methodology underwent rigorous testing on multi-parametric MRI datasets for both brain tumors and strokes. The results demonstrate a significant improvement in addressing critical clinical challenges, including the classification of gliomas, brain metastases, and the prediction of hemorrhagic stroke transformations. Ablation studies further validate the effectiveness of our attention mechanism and feature fusion modules. Discussion: These findings underscore the potential of our approach to meet and exceed current clinical diagnostic demands, offering promising prospects for enhancing healthcare outcomes in the diagnosis and treatment of brain diseases.