Two layers of ancient paddy soil and one modern paddy soil were discovered in archeological excavation of Chuodunshan Relics in Kunshan, China. One of the ancient paddy soils could be ascended to 6 ka BP (prehistoric) and the other to 3 ka BP (Shang-Zhou Period). Two soil profiles, not far apart, named P01 (containing both ancient paddy soil layers and the modern paddy soil layer) and P03 (containing only the latter ancient paddy soil layer and the modern paddy soil layers) respectively, were fixed and soil samples were collected according to soil color and texture. In order to compare the difference of clay mineral characteristics between ancient paddy soils and modern paddy soil, the contents of iron oxides and manganese oxides and the constituents of clay mineral were analyzed. The results showed that there was no difference in total iron content between ancient paddy soils and modern paddy soils. Compared to ancient non-paddy soil (6 ka BP), some of the iron oxides, manganese oxides and smectite were lost in the profile of ancient paddy soil (6 ka BP). The mineral constituents in ancient paddy soil and present paddy soil were very similar, but the contents of 1.4 nm mineral in ancient paddy soil was lower than that of modern paddy soil. The evolution of clay minerals were similar between modern and ancient paddy soils: both were from hydromuscovite to chlorite and vermiculite and then to smectite.