In this study, an innovative strategy, entitled ‘AnnoPRO’, for protein function annotation was thus constructed. First, a novel method enabling image-like protein representations was proposed. This method is unique in capturing the intrinsic correlations among protein features, which can greatly favor the application of the state-of-the-art deep learning methods popular in image classification. Second, a multiscale framework integrating multichannel convolutional neural network and long short-term memory neural network was constructed to realize a deep learning-based protein functional annotation.