On the basis of spatial-temporal perspective, by using the data of farmers’ net income per capita from 1996 to 2007 in counties of Guangxi coupled with the global and local spatial auto-correlation analysis of ESDA and GIS technology, we conduct the empirical research on the rural economic developmental disparity of counties in Guangxi and the evolving characteristics of local spatial heterogeneity. The results show that the rural economic developmental disparity of counties in Guangxi from 1996 to 2007 varies infinitesimally on the whole, and the regions with similar rural economic developmental level have spatial concentrated distribution. Based on these, the local MORAN’S I scatter diagram and LISA concentration diagram are drawn. In comparison with the traditional analytical method, the spatial analytical method of ESDA-GIS can explain the problem of spatial heterogeneity of rural economic development clearly, and have direct visual effect.