Using the method of “Replacing time by space”, based on the analysis of species composition, amount and distribution, ecological dominance and species similarity, and its diversity, the properties of soil seed banks of different land use system which located different ecological evolving sequence including natural forest, secondary forest, shrub grassland, cropland, artificial woodland, abandoned dry field were studied in Beibei, Wushan, Qianjiang and Jinfo Mountain of Nanchuan which belong to Chongqing municipality, a representative karst mountainous region of Three Gorges Reservoir region. The results showed that 68 species germinated in all of 24 plots, most seeds in different land use system soil seed banks are herbage species, and had a obvious connection with above vegetations, indicating that vegetations are at the early stages of succession, degraded seriously. The amount of seeds of xylophyta species decreased and that of herbaceous species which dominated by farmland weeds increased with the increasing of land use intensity. The geographical compositions of herbaceous plants of shrub-grass plot’s soil seed bank indicate that genera of cosmopolitan had a heavy percentage, indicate 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 shrub grass land’s evolution successively. From abandoned cropland, shrub-grass land to secondary forest land, the ecological dominance declined, the diversity and richness indices increased. After the karst slope being cultivated, the soil seed banks of it were destroyed soon. Therefore, the changes of land use pattern are the main threat to the karst secondary vegetation and its soil seed banks in Three Gorges reservoir region.