Schizophrenia (SCZ) is a multifactorial mental illness, thus it will be beneficial for exploring this disease using multimodal data, including functional magnetic resonance imaging (fMRI), genes, and the gut microbiome. Previous studies reported combining multimodal data can offer complementary information for better depicting the abnormalities of SCZ. However, the existing multimodal-based methods have multiple limitations. First, most approaches cannot fully use the relationships among different modalities for the downstream tasks. Second, representing multimodal data by the modality-common and modality-specific components can improve the performance of multimodal analysis but often be ignored. Third, most methods conduct the model for classification or regression, thus a unified model is needed for finishing these tasks simultaneously. To this end, a multi-loss disentangled generative-discriminative learning (MDGDL) model was developed to tackle these issues. Specifically, using disentangled learning method, the genes and gut microbial biomarkers were represented and separated into two modality-specific vectors and one modality-common vector. Then, a generative-discriminative framework was introduced to uncover the relationships between fMRI features and these three latent vectors, further producing the attentive vectors, which can help fMRI features for the downstream tasks. To validate the performance of MDGDL, an SCZ classification task and a cognitive score regression task were conducted. Results showed the MDGDL achieved superior performance and identified the most important multimodal biomarkers for the SCZ. Our proposed model could be a supplementary approach for multimodal data analysis. Based on this method, we could analyze the SCZ by combining multimodal data, and further obtain some interesting findings.