The system functioning and stability for resilience and sustainability has been increasingly concerned with restoration and re-establishment of degraded karst ecosystems in the areas with rock desertification in Southwest China. However, decline in vegetation biomass and nutrient pool has been generally associated with changes in ecosystem functioning and sustainability. To address the relations between biomass, nutrient storage and ecosystem functioning, the partitioning of biomass and major nutrients among the different vegetation pools were studied by a pilot study using a degradation sequence of three karst ecosystems with different degree of vegetation decline from Puding County, Central Guizhou, South West China. The results showed that: (1) there was a decreasing trend both in vegetation biomass above ground and in soil nutrient availability as well as nutrient returning through littering, an increasing trend of fine root biomass and herbaceous biomass with the degradation trend of the ecosystems. The organic matter storage in forest floor was respectively 10 times as the herbaceous biomass and 2 times as the fine root biomass in the forest stand (FO). Whereas, the herbaceous biomass and fine root biomass were 3.5 times and 2.1 times as that of floor organic matter in the shrubland stand (SH), and 2.4 times and 1.4 times as that of floor organic matter in the shrub-and-grassland (SHG) respectively. (2) The nutrient accumulations in ecosystem components varied with the vegetation biomass pattern. The N and P accumulations in forest floor organic matter were significantly higher than that in herbaceous layer and in fine roots in the FO, while the N and P accumulations in herbaceous layer and in fine roots were higher than or similar to that in floor organic matter in the SH and the SHG. (3) There was a sharp decline in nutrient uptake and decomposition percentage, with an increase in percentage of nutrient translocated and returned to soil with the increasing degradation in vegetation from forest to grassland. In particular, the bio-migration and bio-return ratios of N was in the order of SHG > SH > FO, but its uptake and decomposition ratio in order of FO > SHG > SH and FO > SH > SHG respectively. Similarly, the migration and decomposition ratios of P in FO > SHG> SH and FO > SH > SHG, and bio-absorption ratio as SH > FO > SHG, and its bio-return ratio in order of SH > SHG > FO. The results showed that the nutrient return to soil through litterfall was gradually decreased, whereas the biomass of fine roots increased gradually with the increasing trend of vegetation decline. This suggested that major nutrients such as N have undergone a relatively intense translocation and been exhausted in rhizospheric zone for their use in vegetable parts due to loss under vegetation decline in degraded ecosystems. Compared with the forest stand, the shrubland and the shrub-and-grassland have been vulnerable due to lower capability in self-sustaining and regulating under serious disturbances. Finally, it is suggested that the biogeochemical characterization of major nutrients would be an important sector for the functional stability of karst ecosystems.