The fractal structure of root system is the result of phenotypic plasticity of plant root architecture in response to environmental heterogeneity, which reflects the adaptation strategy of plants to the growth environment. The study site was located in Beihaizi National Wetland Park, Jinta county, Gansu province, China (40°13'22″-40°17'2″N, 98°41'24″-98°52'33″E), with the altitude 1215-1261 m and the average annual temperature 9.6 ℃. According to the site conditions, and three kinds of habitats were selected: interdunal depression, gentle sand slope, and slope crest. At the same time, the root fractal structure of Agriophyllum squarrosum was studied by root excavation and win-Rhizo root analyzer. The results showed that the vegetation community height, coverage, aboveground biomass, soil moisture content, compactness and soil bulk density decreased gradually from interdunal depression to slope crest with the change of habitats. As to the Agriophyllum squarrosum population, its density, height and fractal dimension of root system tended to be greater while its fractal abundance smaller. The fractal dimension of Agriophyllum squarrosum root system had a very significantly negative correlation with its fractal abundance in both interdunal depression and slope crest (P < 0.01), as the same in both of gentle sand slope (P < 0.05). The process of the transformation of root configuration from diffusion to density reflects the adaptive mechanism of the plants to deal with various habitat stresses under different site conditions.