The progress in hyperspectral image (HSI) classification owes much to the integration of various deep learning techniques. However, the inherent 3D cube structure of HSIs presents a unique challenge, necessitating an innovative approach for the efficient utilization of spectral data in classification tasks. This research focuses on HSI classification through the adoption of a recently validated deep-learning methodology. Challenges in HSI classification encompass issues related to dimensionality, data redundancy, and computational expenses, with CNN-based methods prevailing due to architectural limitations. In response to these challenges, we introduce a groundbreaking model known as “Crossover Dimensionality Reduction and Multi-branch Deep Learning” (CMD) for hyperspectral image classification. The CMD model employs a multi-branch deep learning architecture incorporating Factor Analysis and MNF for crossover feature extraction, with the selection of optimal features from each technique. Experimental findings underscore the CMD model’s superiority over existing methods, emphasizing its potential to enhance HSI classification outcomes. Notably, the CMD model exhibits exceptional performance on benchmark datasets such as Salinas Scene (SC), Pavia University (PU), Kennedy Space Center (KSC), and Indian Pines (IP), achieving impressive overall accuracy rates of 99.35% and 99.18% using only 5% of the training data.