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Labile organic matter plays an important role in permafrost carbon cycling, however, little is known about the effects of permafrost on labile organic matter dynamics. Here, we examined seasonal changes in the labile organic matter including light fraction carbon (LFC), water extractable organic carbon (WEOC), microbial biomass carbon (MBC) and nitrogen (MBN) contents in a relict permafrost region on the eastern edge of the Qinghai-Tibetan Plateau (QTP), China. We selected three different areas including permafrost, boundary, and seasonally frozen ground area. The results showed that seasonal changes in labile organic matter were not the result of soil heterogeneity. Among all three areas, depth strongly correlated with labile organic matter content. LFC was significantly associated with the soil organic carbon (SOC) content. The MBC contents, which were the lowest in permafrost area but highest in seasonally frozen ground area, were strongly affected by temperature. Multiple linear regression models showed that temperature was a significant predictor for labile organic matter in the permafrost area, but the effects of temperature were weaker in the boundary and seasonally frozen ground areas. Our results suggested that permafrost degradation could decrease production but increase decomposition rates of labile organic matter in permafrost regions, and this process should be taken into consideration in permafrost carbon cycle models.