There are several publications related to the soil organic carbon (SOC) on the Qinghai-Tibetan Plateau (QTP). However, most of these reports were from different parts of the plateau with various sampling depth. Here, we present the results from a systematic sampling and analysis of 200 soil pits. Most of the pits were deeper than 2 m from an east-west transect across the plateau. The SOC and total nitrogen (TN) pools of the 148 × 104 km2, the area of the permafrost zone, for the upper 2 m soils calculated from the vegetation map were estimated to be 17.07 Pg (interquartile range: 11.34-25.33 Pg) and 1.72 Pg (interquartile range: 1.08-2.06 Pg), respectively. We also predicted the distribution of land cover types in 2050 and 2070 using decision tree rules and climate scenarios, and then predicted SOC and TN pools of this region. The results suggested that the SOC and TN pools will decrease in the future. The results not only contribute to the carbon and nitrogen storage and stocks in the permafrost regions as a whole but most importantly, to our knowledge of the possible changes of C and N storage on the QTP in the future.