In the use of method of "Replacing time by space", on the analysis of species composition, amount and distribution, ecological dominance as well as species similarity, and diversity, the properties of soil seed banks of different land use system located in different ecological evolution sequence, including natural forest, secondary forest, shrub grassland, cropland, artificial woodland, abandoned dry field are studied in Beibei, Wushan, Qianjiang and Jifo Mountain of Nanchuan. They are the representative karst mountainous region of the Three Gorges Reservoir region within Chongqing municipality. The results show that 68 species germinated in all of 24 plots. Most seeds in different land use system soil seed banks are herbage species, and have a abvious connection with above vegetations, indicating that vegetations are at the early stages of succession and serious degradation. The amount of seeds of xylophyta species decreased and that of herbaceous species dominated by farmland weeds have increased with the increase of land use intensity. The geographical compositions of herbaceous plants of thrub-grass plot's soil seed bank indicate that genera of cosmopolitan have a heavy percentage, indicating that the growth of herbaceous layer is affected significantly by human being's activities. Therefore, it is important to preserve rare tree species in existing karst vegetation for improving the karst thrub grass land's evolution successively. From abandoned cropland, shrub-grass land to secondary forest land ,the ecological dominance has declined and the diversity and richness indices have increased. After the karst slope being cultivated, the soil seed banks of it have been destroyed soon. Therefore, the changes of land use pattern are the main threat to the karst secondary vegetation and the soil need banks in Three Gorges reservoir region.