Relying on large scale labeled datasets, deep learning has achieved good performance in image classification tasks. In agricultural and biological engineering, image annotation is time-consuming and expensive. It also requires annotators to have technical skills in specific areas. Obtaining the ground truth is difficult because natural images are expensive. In addition, images in these areas are usually stored as multichannel images, such as computed tomography (CT) images, magnetic resonance images (MRI), and hyperspectral images (HSI). In this paper, we present a framework using active learning and deep learning for multichannel image classification. We use three active learning algorithms, including least confidence, margin sampling, and entropy, as the selection criteria. Based on this framework, we further introduce an “image pool” to make full advantage of images generated by data augmentation. To prove the availability of the proposed framework, we present a case study on agricultural hyperspectral image classification. The results show that the proposed framework achieves better performance compared with the deep learning model. Manual annotation of all the training sets achieves an encouraging accuracy. In comparison, using active learning algorithm of entropy and image pool achieves a similar accuracy with only part of the whole training set manually annotated. In practical application, the proposed framework can remarkably reduce labeling effort during the model development and upadting processes, and can be applied to multichannel image classification in agricultural and biological engineering.