Abstract: Identifying microbes associated with diseases is important for understanding the pathogenesis of diseases as well as for the diagnosis and treatment of diseases. In this article, we propose a method based on a multi-source association network to predict microbe-disease associations, named MMHN-MDA. First, a heterogeneous network of multi-molecule associations is constructed based on associations between microbes, diseases, drugs, and metabolites. Second, the graph embedding algorithm Laplacian eigenmaps is applied to the association network to learn the behavior features of microbe nodes and disease nodes. At the same time, the denoising autoencoder (DAE) is used to learn the attribute features of microbe nodes and disease nodes. Finally, attribute features and behavior features are combined to get the final embedding features of microbes and diseases, which are fed into the convolutional neural network (CNN) to predict the microbe-disease associations. Experimental results show that the proposed method is more effective than existing methods. In addition, case studies on bipolar disorder and schizophrenia demonstrate good predictive performance of the MMHN-MDA model, and further, the results suggest that gut microbes may influence host gene expression or compounds in the nervous system, such as neurotransmitters, or metabolites that alter the blood-brain barrier.