In order to explore the development of healthcare in China and the privacy and security risk factors in medical data under the background of big data, the development status of China’s healthcare sector is analyzed. The questionnaire is used to analyze the privacy and security risk factors of healthcare big data and protection measures are put forward based on the data privacy and security risk factors in the context of cloud services in the literature. The results show that in recent years, the number of health institutions, the number of medical personnel, the assets of medical institutions, the per capita hospitalization cost, and the insured population all show a trend of increasing year by year; while in 2017, the crude mortality rate of malignant tumor patients was the highest in China, and the mortality rate of rural patients was higher than that of urban patients. The results of the questionnaire show that the probability of data analysis, medical treatment process, disease diagnosis process, lack of protective measures, and imperfect access system is all greater than 0.8 when medical care big data is oriented to cloud services. Based on this, two levels of privacy protection measures are proposed: technology and management. It indicates that medical institutions need to pay attention to data privacy protection and grasp the use of digital medical data to provide decision support for subsequent medical data analysis. •The development status of China’s healthcare sector is analyzed.•The results of the questionnaire show that the probability of data analysis, medical treatment process, disease diagnosis process, lack of protective measures, and imperfect access system is all greater than 0.8 when medical care big data is oriented to cloud services.•It indicates that medical institutions need to pay attention to data privacy protection and grasp the use of digital medical data to provide decision support for subsequent medical data analysis.