Ecosystem carbon dioxide (CO₂), water vapor, and heat exchanges in alpine wetlands on the Qinghai–Tibetan Plateau are not comprehensively understood. Thus, we studied variability of net ecosystem CO₂ exchange (NEE), ecosystem respiration (Re), gross primary production (GPP), evapotranspiration (ET), and heat fluxes over a headwater wetland ecosystem in the Qinghai Lake region. Results showed that the headwater wetland ecosystem was net CO₂ absorption on the annual scale, in which monthly NEE, GPP, and Re in two consecutive years varied from -165.16 to 93 g CO₂ m^-2 mo^-1, 6.66 to 384.45 g CO₂ m^-2 mo^-1, and 6.9 to 232.02 g CO₂ m^-2 mo^-1, respectively. The monthly ET from June to September was smaller than precipitation; these results reversed in the remaining months. Annual ET was 362.1 mm in 2015 and 324.96 mm in 2016. The net radiation (R_n), sensible heat (H), latent heat (LE), and ground heat (G) fluxes showed similar monthly patterns. Values of monthly average half-hour R_n, H, LE, and G at the daytime showed R_n > LE > H > G, and the time of the monthly half-hour G peak obviously lagged the R_n, H, and LE. Monthly average Bowen ratios were <1 from May to October, but it reversed in the rest of the months.