Based on digital figures of Guangzhou ecological security assessment which were contributed by the authors, the spatial-temporal heterogeneities of ecological security characteristics were analyzed by geo-statistic methods, including analysis of spatial self-relations and scale effectiveness, spatial heterogeneity and temporal dynamics of semi-variation of ecological security, and directional difference of ecological security characteristics. The paper had got the following important results: Spatial heterogeneity of regional ecological security of Guangzhou was great. The ecological security was lowest in the city center, and highest in Zengcheng. But the temporal variation was biggest in Zengcheng. A scale effectiveness of self-relations of ecological security was revealed, and the classification number 3 was sensitive scale. It′s obvious that the scale effectiveness of classification number was also temporal difference. The analysis of self-relations for Guangzhou ecological security heterogeneity revealed that spatial heterogeneity, temporal difference and directional difference were simultaneously representative. In those above, spatial heterogeneity was most important. It showed that ecological protection and economical development had been progressed in the period of 1990-2005 in Guangzhou.