Obtaining a protein's 3D structure is crucial to the understanding of its functions and interactions with other proteins. It is critical to accelerate the protein crystallization process with improved accuracy for understanding cancer and designing drugs. Systematic high-throughput approaches in protein crystallization have been widely applied, generating a large number of protein crystallization-trial images. Therefore, an efficient and effective automatic analysis for these images is a top priority. In this paper, we present a novel system, CrystalNet, for automatically labeling outcomes of protein crystallization-trial images. CrystalNet is a deep convolutional neural network that automatically extracts features from X-ray protein crystallization images for classification. We show that (1) CrystalNet can provide real-time labels for crystallization images effectively, requiring approximately 2 seconds to provide labels for all 1536 images of crystallization microassay on each plate; (2) compared with the state-of-the-art classification systems in crystallization image analysis, our technique demonstrates an improvement of 8% in accuracy, and achieve 90.8% accuracy in classification. As a part of the high-throughput pipeline which generates millions of images a year, CrystalNet can lead to a substantial reduction of labor-intensive screening.