Based on the spatial autocorrelation (SA) and Geographic Information System (GIS) technology, the spatial differences of the rural economic development level was investigated by adopting the rural resident income data in Guizhou Province from 2009 to 2013. The results of global Moran’s I value for rural resident income at county level showed that there existed significant positive spatial autocorrelation and significant spatial aggregation in the spatial distribution of rural resident income. However, the global Moran’s I value showed the increasing trend during 2009 to 2013, indicating an enlarged spatial disparity of rural economy in Guizhou. The results of the local indicators of spatial association(LISA) cluster maps of 2009 and 2013 showed that most of counties were characterized by positive local spatial association , ie. They were located in the HH or the LL region. The significant HH counties were mostly to be found in the middle part of Guizhou. The significant LL counties were found in the Wuchuan county and Zhenfeng county, northwest and southwest of Guizhou.