Recently, convolutional neural network (CNN)-based classification models have shown good performance for motor imagery (MI) brain-computer interfaces (BCI) using electroencephalogram (EEG) in end-to-end learning. Although a few explainable artificial intelligence (XAI) techniques have been developed, it is still challenging to interpret the CNN models for EEG-based BCI classification effectively. In this research, we propose 3D-EEGNet as a 3D CNN model to improve both the explainability and performance of MI EEG classification. The proposed approach exhibited better performances on two MI EEG datasets than the existing EEGNet, which uses a 2D input shape. The MI classification accuracies are improved around 1.8% and 6.1% point in average on the datasets, respectively. The permutation-based XAI method is first applied for the reliable explanation of the 3D-EEGNet. Next, to find a faster XAI method for spatio-temporal explanation, we design a novel technique based on the normalized discounted cumulative gain (NDCG) for selecting the best among a few saliency-based methods due to their higher time complexity than the permutation-based method. Among the saliency-based methods, DeepLIFT was selected because the NDCG scores indicated its results are the most similar to the permutation-based results. Finally, the fast spatio-temporal explanation using DeepLIFT provides deeper understanding for the classification results of the 3D-EEGNet and the important properties in the MI EEG experiments.