The sensitivity of soil carbon and nitrogen to warming is a major uncertainty in projections of climate. However, previous studies about soil organic carbon (SOC) stocks and potential emission predominantly concentrated on the shallow soil layer in high latitude ecosystems. In this study, we analyzed the SOC, total nitrogen (TN) and soil inorganic carbon (SIC) stocks, C/N ratios, and stable carbon isotope (δ¹³C) in the active layer and permafrost layer on the Eboling Mountain in the upper reach of Heihe River basin, northwestern China. Our results showed that the average stocks of SOC, TN, and SIC in permafrost layer above soil parent materials (71.7 kg m^-2, 8.0 kg m^-2, 34.7 kg m^-2) were much higher than those in the active layer (44.3 kg m^-2, 5.3 kg m^-2, 12.2 kg m^-2). The δ¹³C pattern in the soil profiles indicated that historical drainage conditions and pedogenesis were important factors in determining soil organic matter (SOM) stocks in this permafrost region. The δ¹³C and C/N ratios of the transient layer and some layers of permafrost implied that the degradation of SOM was different. These results highlight that carbon and nitrogen in permafrost regions with Alpine Kobresia meadow could make significant contribution to China's terrestrial carbon cycle.