The invention discloses a medical insurance big data based analysis method for measuring and calculating the incidence of rare diseases, and relates to medical insurance data processing and analysis technologies. Measured and calculated diseases are diseases that cannot be completely cured, so that people have to suffer from the diseases for life long time if the diseases are diagnosed. Numeratorand denominator information required by incidence calculation can be obtained by summarizing multiple key parameters of medical insurance data every month, so that the incidence can be obtained through calculation, wherein the numerator is the number of new cases of a target disease in a certain range of population within specific time, and the denominator is the number of exposed populations within the specific time, that is, people may have the target disease, but people, which have already had the disease and cannot become the new cases, need to be excluded. The incidence data can be obtained through the method, so that the development of epidemiological study of rare diseases can be promoted, and data and technology support can be provided for the reasonable making of clinical guidelines; and conversion applications of medical insurance big data can be further promoted, and the blank of epidemiological data on rare diseases in China can be filled up.