Graph neural networks (GNNs) provide powerful insights for brain neuroimaging technology from the view of graphical networks. However, most existing GNN-based models assume that the neuroimaging-produced brain connectome network is a homogeneous graph with single types of nodes and edges. In fact, emerging studies have reported and emphasized the significance of heterogeneity among human brain activities, especially between the two cerebral hemispheres. Thus, homogeneous-structured brain network-based graph methods are insufficient for modelling complicated cerebral activity states. To overcome this problem, in this paper, we present a heterogeneous graph neural network (HebrainGNN) for multimodal brain neuroimaging fusion learning. We first model the brain network as a heterogeneous graph with multitype nodes (i.e., left and right hemispheric nodes) and multitype edges (i.e., intra- and interhemispheric edges). Then, we propose a self-supervised pretraining strategy based on a heterogeneous brain network to address the potential overfitting problem caused by the conflict between a large parameter size and a small medical data sample size. Our results show the superiority of the proposed model over other existing methods in brain-related disease prediction tasks. Ablation experiments show that our heterogeneous graph-based model attaches more importance to hemispheric connections that may be neglected due to their low strength by previous homogeneous graph models. Other experiments also indicate that our proposed model with a pretraining strategy alleviates the problem of limited labelled data and yields a significant improvement in accuracy.