With the development of big data and medical information control system, electronic medical records sharing across organizations for better medical treatment and advancement has attracted much attention both from academic and industrial areas. However, the source of big data, personal privacy concern, inherent trust issues across organizations and complicated regulation hinder the great progress of healthcare intelligence. Blockchain, as a novel technique, has been used widely to resolve the privacy and security issues in electronic medical records sharing process. In this paper, we propose a hybrid blockchain–based electronic medical records sharing scheme to address the privacy and trust issues across the medical information control systems, rendering the electronic medical records sharing process secure, effective, relatively transparent, immutable, traceable and auditable. Considering the above confidential issues, we use different sharing methods for different parts of medical big data. We share privacy-sensitive couples on the consortium blockchain, while sharing the non-sensitive parts on the public blockchain. In this way, authorized medical information control systems within the consortium can access the data on it for precise medical diagnosis. Institutions such as universities and research institutes can get access to the non-sensitive parts of medical big data for scientific research on symptoms to evolve medical technologies. A working prototype is implemented to demonstrate how the hybrid blockchain facilitates the pharmaceutical operations in a healthcare information control ecosystem. A blockchain benchmark tool Hyperledger Caliper is used to evaluate the performance of hybrid blockchain–based electronic medical records sharing scheme on throughput and average latency which proves to be practicable and excellent.