Hashing-based medical image retrieval has drawn extensive attention recently, which aims at providing effective aided diagnosis for medical personnel. In the paper, a novel deep hashing framework is proposed in the medical image retrieval, where the processes of deep feature extraction, binary code learning, and deep hash function learning are jointly carried out in supervised fashion. Particularly, the discrete constrained objective function in the hash code learning is optimized iteratively, where the binary code can be directly solved with no need for relaxation. In the meantime, the semantic similarity is maintained by fully exploring supervision information during the discrete optimization, where the neighborhood structure of training data is preserved by applying a graph regularization term. Additionally, to gain the fine-grained ranking of the returned medical images sharing the same Hamming distance, a novel image re-ranking scheme is proposed to refine the similarity measurement by jointly considering Euclidean distance between the real-valued feature descriptors and their category information between those images. Extensive experiments on the pulmonary nodule image dataset demonstrate that the proposed method can achieve better retrieval performance over the state of the arts.