Purpose/Significance Aiming at the pain points that are easy to leak patient privacy in internet self-service medical diagnosis, a set of secure data privacy protection scheme is designed to protect patients’ medical and health data and provide accurate diagnosis and treatment suggestions. Method/Process The disease data stored by the medical institutions and the patients’ medical and health data are processed by homomorphic encryption and privacy protection control technology and uploaded to the cloud server. The cloud server calculates the similarity between the patients’ medical and health data and the disease data of the medical institutions and matches the patients’ disease condition to send the therapies to the patients. Result/Conclusion The medical data privacy protection scheme based on homomorphic encryption and privacy protection access control can effectively protect patients’ privacy in internet self-service medical diagnosis, and provide accurate medical diagnosis and treatment recommendations.