The rock desertification in karst mountains is a kind of land degradation processes correlated with vulnerable eco-geology background and human activities. This paper chooses the typical karst mountains in Chongqing as an example to discuss the impact of different land use patterns on mechanical composition of soil, waterstable aggregates, soil organic matter, the compositions of soil seed banks and bio-diversity of karst ecosystem. The results show that the surface soil layer sandification is more evident after the reclamation, the more intensive land utilization, the more serious the destruction on soil aggregate structure. The soils of woodland and grassland systems have not only a superior soil water retention property but also a soil wate-rsupplying capacity than the soils with intense land utilization, and the soil organic matter is impressed by land using intensity distinctly. The amount of seeds of xylophyta species decreases with the increase in strength of land use, while the amount of seeds of herbaceous species increase, and most are farmland weeds. The changes of land use patterns have the dominant influence on secondary vegetation and their soil seed banks.