Territorial spatial planning is a planning system of multi planning integration of main function area planning, land use planning, urban and rural planning. The territorial spatial planning system, as a basic platform for the comprehensive integration of GIS theory and technology throughout the whole process, provides strong support for multiple links such as technical standards, basic research, planning preparation, and information platform construction. In the context of territorial spatial planning system construction in China, facing the old and new problems in the teaching of urban and rural planning GIS courses, strengthening the foundation is an effective way to leverage the supporting role of GIS courses in the territorial spatial planning system. The GIS course for urban and rural planning must further strengthen its fundamental supporting role in planning, and strengthen the teaching of GIS basic theories and methods. The teaching content, teaching methods and teaching organization need to innovate actively and keep pace with the times, seek the teaching emergency way that connects with the territorial spatial planning system of the new era, and constantly improve the students’ technical practical ability and innovative thinking ability, so as to cultivate practical and innovative talents who meet the needs of the territorial spatial planning system in the new era.