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Peatland fires are frequent, but the effect of fire on soil organic carbon in peatlands is still currently variable. Especially at long time scales, it has not been clarified. In order to reveal the relationship between carbon accumulation patterns in peatlands at long time scales in response to local fire changes, high-resolution peat sediments from peatlands in the Three River Plain were selected and analysed for stratified charcoal debris and organic carbon in this paper. The results showed that the stronger carbon sequestration capacity in the periods of 0.6, 0.75, 1.25, 2.3, 2.75, 2.9, 3.6 and 5 ka BP corresponded to weaker fire intensity or even no fire. Late-Holocene fires in the Sanjiang Plain reduced the rate of carbon sequestration, suggesting that fires have been an important driver of the reduction in carbon sequestration capacity over the last 6000 years.