Fractal study is one of the most important branches in modern theoretic geography. This paper commenced with the application of the fractal theory and tried to compare the characteristics of the settlements system at the scale of which contains county, town and village, by using ArcGIS9.3 software and taking national results of the second national land survey data as the main data source. The study area was located in Danyang and Jurong of Zhenjiang. Based on the fractal theory, the paper studied the scale difference of spatial structure of settlements system, then the paper analyzed the influencing factor of spatial aggregation fractal character of the rural settlements at the scale of town and village. According to the results of calculation and analysis, the paper drew the conclusions below:(1) settlements system in Danyang and Jurong are fractal in spatial structure of settlements system, acting as a self-similar structure;(2) The spatial aggregation of rural settlements system in Danyang and Jurong both act as fractal character at different scale;(3) as a result of spatial overlay between terrain and fractal dimension, statistical results shows that terrain is a important factor which influence the spatial aggregation;(4) At the scale of the town hinterland, we found that improvement of transportation network makes the rural settlements more independent on spatial distances. Therefore, in the future work, fractal theory would be a useful tool for the planning of settlements system, finally making effective use of geospatial resources and optimizing the spatial structure of the settlement system in a specific area