Soil organic carbon (SOC) and total nitrogen (TN) stocks are usually calculated with samples collected using core samplers. Although the calculation considers the effects of gravel in soil samples, other coarse fragments such as stones or boulders in soil may not be collected due to the restricted diameter of core samplers. This would cause an incorrect estimation of soil bulk density and ultimately SOC and TN stocks. In this study, we compared the relative volume of coarse fragment and bulk density of fine earth determined by large size soil sampler with three core samplers. We also investigated the uncertainties in estimation of SOC and TN stocks caused by this soil sampler procedure in three typical alpine grasslands on the northeast edge of the Qinghai-Tibetan Plateau ( QTP), China. Results show that (1) the relative volume and size of coarse fragment collected by large size sampler were significantly ( p <0.05) higher and larger than those of core samplers, while bulk density of fine earth, SOC and TN stocks show opposite patterns in all grassland types; (2) SOC and TN stocks determined by core samplers were 17%- 45% and 18%- 46% higher than larger size sampler for three typical alpine grasslands; and (3) bulk density of fine earth, SOC and TN stocks exponentially decreased with the increasing of coarse fragment content. We concluded that core sampler methods significantly underestimated the volume occupied by coarse fragment but overestimated SOC and TN stocks. Thus, corrections should be made to the results from core samplers using large size samplers on regions with gravel and stone-rich soils in future studies.