Electroencephalography (EEG) motor imagery (MI) signals have recently attracted much attention because of their potential to communicate with the surrounding environment in a specific way without the need for muscular and physical movement. Despite these advantages, these signals are difficult to detect due to their low signal to noise (SNR) rate and non-stationary and dynamic nature. Convolutional neural networks (CNN) can extract appropriate spatial and temporal features without the need for separate feature extraction and classification steps. Clean input data for CNN significantly improves its performance, but sometimes, common interference occurs between multi-channel signals. This challenge, along with the noisy EEG signals, degrades the performance of CNN networks. This paper presents a channel selection method based on convolutional neural networks to obviate these challenges. The proposed shallow convolutional neural network (SCNN) is designed with temporal convolution and pointwise convolution (using 1×1 convolution) to select the best channel with minimal computational load. Following the channel selection step, the multi-layer fusion CNN model was used to classify the signals. Choosing suitable and relevant EEG channels for motor imagery tasks makes it possible to create appropriate inputs for the classification model so that the model can be improved in the end. For High Gamma Dataset and Brian-Computer Interface (BCI) Competition IV-2a, the following accuracies were obtained: 81.15% and 72.01%, which are higher than when the other channel selections such as Mutual Information, Sequential Feature Forward Selection (SFFS) and wrapper methods are used.