Benefitting from the low storage cost and high retrieval efficiency, hash learning has become a widely used retrieval technology to approximate nearest neighbors. Within it, the cross-modal medical hashing has attracted an increasing attention in facilitating efficiently clinical decision. However, there are still two main challenges in weak multi-manifold structure perseveration across multiple modalities and weak discriminability of hash code. Specifically, existing cross-modal hashing methods focus on pairwise relations within two modalities, and ignore underlying multi-manifold structures across over 2 modalities. Then, there is little consideration about discriminability, i.e., any pair of hash codes should be different. In this paper, we propose a novel hashing method named multi-manifold deep discriminative cross-modal hashing (MDDCH) for large-scale medical image retrieval. The key point is multi-modal manifold similarity which integrates multiple sub-manifolds defined on heterogeneous data to preserve correlation among instances, and it can be measured by three-step connection on corresponding hetero-manifold. Then, we propose discriminative item to make each hash code encoded by hash functions be different, which improves discriminative performance of hash code. Besides, we introduce Gaussian-binary Restricted Boltzmann Machine to directly output hash codes without using any continuous relaxation. Experiments on three benchmark datasets (AIBL, Brain and SPLP) show that our proposed MDDCH achieves comparative performance to recent state-of-the-art hashing methods. Additionally, diagnostic evaluation from professional physicians shows that all the retrieved medical images describe the same object and illness as the queried image.