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Data mining, data prediction and all-round digital monitoring of health big data make the dilemma of personal privacy control prominent. The weakening of the control of personal privacy by big data technology, the people’s data belief, the diversity of interests and the conflict of interests are the main causes of the problem of personal privacy in the context of the application of health big data. Therefore, in the application of health big data, the solution to the problem of personal privacy in the context of health big data application is to enhance the value transparency of big data technology, return and reshape humanism, and explore common values to reduce conflicts of interest.