Taiwan is one of few countries in the world that execute national health insurance system. Having the complete population-based medical records, the National Health Insurance Research Database (NHIRD) allows the researchers to study and evaluate useful medical information by using biological statistics and data mining techniques. Our research will constructed the system flow for epidemiological studies used in systemic lupus erythematosus (SLE) and asthma disease, it consists four steps in our study. To use system flow make in different environment, seasons for research in epidemiological characteristics, which can reduce research time and conduct research efficiently. Hundreds and Thousands of raw medical records had been stored and saved in the NHIRD system, which could also bring huge scientific impact for medical researchers since those records are not fully understood, evaluated, and practiced yet. Lastly, with NHIRD system the collaboration between medical researchers and the dedicated doctors on given diseases can be of great support to enhance the medical database in Taiwan.