The paper introduces the application of geographic information system (GIS) in medical science areas at home and abroad; taking Beijing Health Bureau administration GIS construction as application examples, it sorts out Beijing Health Bureau geographic information resources, investigates the needs of related government departments and public services. Based on these the paper analyzes the construction contents and basic functions of the system, describes the overall steps of Beijing Health Bureau administration GIS construction and the design of Beijing health care organization GIS maps which are firstly constructed.