Brain–computer interface (BCI) technology holds promise for individuals with profound motor impairments, offering the potential for communication and control. Motor imagery (MI)-based BCI systems are particularly relevant in this context. Despite their potential, achieving accurate and robust classification of MI tasks using electroencephalography (EEG) data remains a significant challenge. In this paper, we employed the Minimum Redundancy Maximum Relevance (MRMR) algorithm to optimize channel selection. Furthermore, we introduced a hybrid optimization approach that combines the War Strategy Optimization (WSO) and Chimp Optimization Algorithm (ChOA). This hybridization significantly enhances the classification model’s overall performance and adaptability. A two-tier deep learning architecture is proposed for classification, consisting of a Convolutional Neural Network (CNN) and a modified Deep Neural Network (M-DNN). The CNN focuses on capturing temporal correlations within EEG data, while the M-DNN is designed to extract high-level spatial characteristics from selected EEG channels. Integrating optimal channel selection, hybrid optimization, and the two-tier deep learning methodology in our BCI framework presents an enhanced approach for precise and effective BCI control. Our model got 95.06% accuracy with high precision. This advancement has the potential to significantly impact neurorehabilitation and assistive technology applications, facilitating improved communication and control for individuals with motor impairments