In order to understand the carbon fate of alpine peatlands under climate change, this study aimed to measure carbon accumulation in recent decades and that during the Holocene at seven representative peat sites on the Zoige Plateau using empirical peat core data (14C and 137CS) and modeling approaches. The observed apparent carbon accumulation rate over the past 50 years was 75 (35–123) g C m−2 yr−1, nearly four times that of 19 (7–30) g C m−2 yr−1over the whole Holocene. With decomposition history included in consideration by using modeling approaches, the average expected peat carbon accumulation rate was still nearly 1.6 times that of the modeled net carbon uptake rate of peats accumulated over the whole Holocene, though exceptions were found for Denahequ and Hongyuan peat cores with extremely low water table levels. The newly accumulated peat carbon of the Zoige Plateau amounted to 0.4 Tg C yr−1 (1 Tg = 1012 g) during recent decades. Overall, the effect of climate warming on recent C accumulation of peatlands on the Zoige Plateau is dependent on their water conditions. The peat C storage on the alpine Plateau is threatened by human activities (drainage) and continuous climate change with increasing temperature and decreasing precipitation which cause dryness of peatlands.