Abstract: The pedogenic rock is the material basis for the soil formation and development, and its rock formation type provides important constraints for the element geochemical characteristics of the soil. For the soils originated from various types of rock formation in Xin’an River Basin, the ecological geochemical survey was carried out in the small watershed as the investigation unit. A comparative study of soils and corresponding parent rocks at different horizons under different geological settings was systematically conducted, obtaining the distribution and partitioning characteristics of major elements, nutrient elements, heavy metal elements and other beneficial elements in soil layer, parent material layer and pedogenic rock of the main rock formation in Xin’an River Basin. The results indicate consistent geochemical characteristics of various elements in the soil, parent material and pedogenic rock. The composition and distribution of most elements in the soil of Xin’an River Basin are apparently controlled by the rock formation type of their pedogenic rock, except some major elements and pH values showing minor difference among the soils sourced from different rock formations. The soil developed from black rock series and carbonate rock is the most different from the background of the whole region, which is significantly enriched with sulphophile elements such as Cd, Cu, Se, Mo, existing a certain environmental quality risk. The soil derived from red beds is generally lack of N, P and organic matter, while that from volcanic rocks and granite is generally rich in K. The geochemical characteristics of the soil elements come from clastic rocks and metamorphic rocks are slightly different from the background of the whole basin.