With the continuous development of big data, improving online medical insurance service system becomes an important part of hospital management and development, facilitating the development and application of hospital medical insurance service system. The paper first focuses on the problems of hospital online medical insurance service system. Secondly, it expounds the solutions to system development. Finally, this paper discusses the achievement of online inquiry of outpatient prescriptions, the informatization application of medical insurance archives system, intelligent assisted auditing system of medical insurance and big data privacy protection.