Peatlands are characterized by their large carbon storage capacity and play an essential role in the global carbon cycle. However, the future of the carbon stored in peatland ecosystems under a changing climate remains unclear. In this study, based on the eddy covariance technique, we investigated the net ecosystem CO2 exchange (NEE) and its controlling factors of the Hongyuan peatland, which is a part of the Ruoergai peatland on the eastern Qinghai-Tibet Plateau (QTP). Our results show that the Hongyuan alpine peatland was a CO2 sink with an annual NEE of -226.61 and -185.35 g C m(-2) in 2014 and 2015, respectively. While, the non-growing season NEE was 53.35 and 75.08 g C m(-2) in 2014 and 2015, suggesting that non-growing seasons carbon emissions should not be neglected. Clear diurnal variation in NEE was observed during the observation period, with the maximum CO2 uptake appearing at 12:30 (Beijing time, UTC+8). The Q(10) value of the non-growing season in 2014 and 2015 was significantly higher than that in the growing season, which suggested that the CO2 flux in the non-growing season was more sensitive to warming than that in the growing season. We investigated the multi-scale temporal variations in NEE during the growing season using wavelet analysis. On daily timescales, photosynthetically active radiation was the primary driver of NEE. Seasonal variation in NEE was mainly driven by soil temperature. The amount of precipitation was more responsible for annual variation of NEE. The increasing number of precipitation event was associated with increasing annual carbon uptake. This study highlights the need for continuous eddy covariance measurements and time series analysis approaches to deepen our understanding of the temporal variability in NEE and multi-scale correlation between NEE and environmental factors.