GIS system is excellent at digging out and utilizing information of space, being able to collect, store, manipulate, retrieve and display space information recognized by position. GIS not only provides decision-makers with related information concerning location and distribution of public facilities, but also provides a nice visual tool to describe the background and structure of a problem. The most important point is that an analysis of alternative programs created by GIS would optimize decision-making. GIS technology is applied here to study the layout and structure of the higher education in Yunnan Province, analyzing the changes of Yunnan higher education's spatial layout structure from several aspects, such as the layout of college, scale of higher education, the relationship between the development of colleges and economy and population, exploring the relationships between higher education resource and relevant factors including geographical environment, population, economy, and so on, in order to provide scientific supports for decision-making concerning rational planning issues of spatial resources distribution of higher education in Yunnan Province, and to provide technical support for the scientific development of higher education.