ObjectiveTo explore the methods of data management and statistical analysis for longitudinal big data collected from mobile health management applications (APP). MethodsThe data management process and statistical analysis method were proposed by summarizing the characteristics of the data from mobile health management APPs. The methods would be clarified by a practical case: an APP recording female menstruation. ResultsThe data from health management APPs belong to longitudinal big data and the original record of the APP should be reprocessed or computed before conducting statistical analysis. A two-step data cleaning procedure was suggested for data management of the original records and reprocessed data, and longitudinal models such as mixed models was recommended for statistical analysis. ConclusionsThe data from health management APPs could be used for medical research via specific data management and statistical analysis after removing suspicious data. Cloud computing could be a viable method to improve efficiency of the big data analysis of health management APPs.