Class imbalance is a key issue for the application of deep learning for remote sensing image classification because a model generated by imbalanced samples training has low classification accuracy for minority classes. In this study, an accurate classification approach using the multistage sampling method and deep neural networks was proposed to classify imbalanced data. We first balance samples by multistage sampling to obtain the training sets. Then, a state-of-the-art model is adopted by combining the advantages of atrous spatial pyramid pooling (ASPP) and Encoder-Decoder for pixel-wise classification, which are two different types of fully convolutional networks (FCNs) that can obtain contextual information of multiple levels in the Encoder stage. The details and spatial dimensions of targets are restored using such information during the Decoder stage. We employ four deep learning-based classification algorithms (basic FCN, FCN-8S, ASPP, and Encoder-Decoder with ASPP of our approach) on multistage training sets (original, MUS1, and MUS2) of WorldView-3 images in southeastern Qinghai-Tibet Plateau and GF-2 images in northeastern Beijing for comparison. The experiments show that, compared with existing sets (original, MUS1, and identical) and existing method (cost weighting), the MUS2 training set of multistage sampling significantly enhance the classification performance for minority classes. Our approach shows distinct advantages for imbalanced data.