Although the Qinghai-Tibetan Plateau (QTP) has experienced striking warming during the past century, information on how soil carbon (C) and nitrogen (N) pools of the alpine regions on the QTP respond to long-term warming is scarce. The aims of this study were to assess the response of soil organic C (SOC), total N (TN), labile C and N – including microbial biomass C (MBC) and N (MBN), inorganic N (N_inorg), dissolved organic C (DOC), and N (DON) – to 15-year experimental warming in an alpine region (Kobresia meadow and Potentilla scrubland), on the northeastern QTP using open-top chambers (OTCs). Fifteen-year experimental warming had no effect on SOC and TN concentrations and storage at 0-30 cm soil depth, either in Kobresia meadow or Potentilla scrubland habitat, which might be related to the low temperature increase and the unchanged water content. Long-term warming obviously affected soil labile C and N and their contributions to SOC and TN, especially in the meadow habitat, but the values were low, thus the variation of the labile C and N was not enough to influence total C and N storage. The C and N pools were shown to be controlled by different controlling factors, and scrubland was more stable than the meadow ecosystem confronting the change of environment.