The objective of this study is to investigate the effect of decreased permafrost stability on carbon storage of the alpine ecosystems in the northeastern margin of the Qinghai–Tibet Plateau. During July and August 2013, we selected 18 sites in five types of permafrost (stable, substable, transitional, unstable, and extremely unstable) regions. We measured aboveground phytomass carbon (APC) and soil respiration (SR), soil inorganic carbon (SIC), soil organic carbon (SOC), belowground phytomass carbon, and soil properties down to 50 cm at same types of soils and grasslands. The results indicated that ecosystem carbon in cold calcic soils first decreased and then increased as the permafrost stability declined. Overall, decreasing permafrost stability was expected to reduce ecosystem carbon in meadows, but it was not obvious in swamp meadows and steppes. APC decreased significantly, but SIC and SOC in steppes first decreased and then increased with declining permafrost stability. Soil clay fraction and soil moisture were the controls for site variations of ecosystem carbon. The spatial variations in SR were possibly controlled by soil moisture and precipitation. This meant that alpine ecosystems carbon reduction was strongly affected by permafrost degradation in meadows, but the effects were complex in swamp meadows and steppes.