Abstract: In real life, the patient's EMR(electronic medical record) is usually managed by the hospital, and the EMR data are also stored by the EMR management system. This kind of centralized storage method will make the patient's privacy information exist the risk of leakage when sharing information across hospitals. Starting with the key technology of information security-digital encryption technology, the classical symmetric encryption algorithm (data encryption standard, DES) and asymmetric encryption algorithm (Rivest-Shamir-Adleman,RSA) were analyzed, and a hybrid encryption scheme was proposed for medical data security storage, improving the security limitations in data encryption and proposes. Firstly, an improved algorithm IBDES was proposed to enhance the security strength by double encryption. Secondly, an improved algorithm EPNRSA was proposed to reduce the time complexity of RSA encryption and ensure the security quality of encryption. Thirdly, a hybrid encryption scheme based on IBDES and EPNRSA was formed. Finally, theoretical analysis and simulation experiments were carried out.The results show that the scheme can provide a better encryption and decryption effect, fast execution speed and high security, being an ideal method for medical data security storage.