The atmospheric information obtained by airborne environmental atmospheric composition detecting system is closely related to the spatial position. The master control system of atmospheric composition detecting system is designed to integrate geographic information system (GIS) to improve detecting precision and provide accurate spatial reference information for subsequent data inversion. By using the functions of spatial data management, analysis, graphical display and output of GIS, this system has achieved flight route planning, visual display of route, real-time path tracking and geographical data storage which provides a certain reference for the operator.