In brain–computer interface (BCI) systems, motor imagery (MI) electroencephalogram (EEG) is widely used to interpret the human brain. However, MI classification is challenging due to weak signals and a lack of high-quality data. While deep learning (DL) methods have shown significant success in pattern recognition, their application to MI-based BCI systems remains limited. To address these challenges, we propose a novel deep learning algorithm that leverages EEG signal features through a two-branch parallel convolutional neural network (CNN). Our approach incorporates different input signals, such as continuous wavelet transform, short-time Fourier transform, and common spatial patterns, and employs various classifiers, including support vector machines and decision trees, to enhance system performance. We evaluate our algorithm using the BCI Competition IV dataset 2B, comparing it with other state-of-the-art methods. Our results demonstrate that the proposed method excels in classification accuracy, offering improvements for MI-based BCI systems.