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Soil carbon and nitrogen storage and stabilization are the key to solving the problems of mitigation of global warming and maintaining of crop productivity. In this study, the contents of soil organic carbon (SOC) and soil organic nitrogen (SON) and their stable isotope compositions (C-13(SOC) and N-15(SON)) in soil profiles were determined in two agricultural lands (including a farmland and an abandoned farmland) and four non-agricultural lands (including two shrub-grass lands and two shrub lands) in the karst critical zone observatory (CZO), Southwest China. The contents of SOC and SON were used for research on the effects of land use on SOC and SON storage, and the change of C-13(SOC) and N-15(SON) values in soil profiles were used to indicate SOC and SON stabilization. The results showed that agricultural activities reduced SOC and SON storage in the whole soil layers of farmland compared to non-agricultural lands, and farmland abandonment slightly increased SOC and SON storage. Crop rotation between peanut (C-3) and corn (C-4) affected the C-13(SOC) in surface soils of agricultural lands (-21.6 parts per thousand), which were intermediate between shrub lands (-22.7 parts per thousand) and shrub-grass lands (-19.6 parts per thousand). N-15-depleted SON in surface soils in farmland compared to those soil in other lands possibly associated with synthetic N fertilizer application. In soil layers below 30 cm depth the C-13(SOC) deceased with depth, while the N-15(SON) displayed irregular fluctuation. The change in C-13(SOC) and N-15(SON) through soil profiles in karst soils were more intensive than those in semiarid grassland soils indicating the less stabilization of SOC and SON in karst soils.