Recently developed hybrid models that stack 3D with 2D CNN in their structure have enjoyed high popularity due to their appealing performance in hyperspectral image classification tasks. On the other hand, biological genome graphs have demonstrated their effectiveness in enhancing the scalability and accuracy of genomic analysis. We propose an innovative deep genome graph-based network (GGBN) for hyperspectral image classification to tap the potential of hybrid models and genome graphs. The GGBN model utilizes 3D-CNN at the bottom layers and 2D-CNNs at the top layers to process spectral–spatial features vital to enhancing the scalability and accuracy of hyperspectral image classification. To verify the effectiveness of the GGBN model, we conducted classification experiments on Indian Pines (IP), University of Pavia (UP), and Salinas Scene (SA) datasets. Using only 5% of the labeled data for training over the SA, IP, and UP datasets, the classification accuracy of GGBN is 99.97%, 96.85%, and 99.74%, respectively, which is better than the compared state-of-the-art methods.