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By selecting the per capita GDP of every county, this article uses the methods of exploratory spatial data analysis, Kiging spatial interpolation, semivariogram function, and the software of ArcGIS 10.0, Geoda and SPSS to show the spatial-temporal evolution of economic disparities at county level in Guangdong province from 1991 to 2013. The results show that: the economy of Guangdong province at county level presents a positive autocorrelation. It appears a downward trend in 2004, but it goes on growing at a steady trend. Cold-spot areas are dispersed in the north of Guangdong Province and the individual counties of East and West wings, while the hot-spot areas are mainly concentrated in the Pearl River Delta Center. Through the analysis of semivariogram function, it finds that the spatial self-organization of the county economy of Guangdong Province is getting stronger and the spatial random component of different pattern is in the smaller proportion. The main factors are due to the difference of natural conditions in regional economy, geographical conditions and regional development policy.