The course of geographic information system principle and application is an important basic course for the major in geographic information system, surveying and mapping, resources and environment, urban and rural planning and management as well as geographic science, as a result, their experiment teaching occupies an important place in the whole process of teaching. According to currently main problems in experiment teaching of this course, this paper studies reform and practice in teaching system from such three aspects as the construction of comprehensive system of experiment teaching, experiment course and teaching multimedia courseware draw-up as well as innovative open experiment setup in order to provide corresponding security for cultivating students’ practical ability and innovative ability.