A comprehensive understanding of the absorption and emission characteristics of greenhouse gases is vital to estimating carbon budget in lakes. For the Poyang Lake, most efforts have been devoted to the study of wetland vegetation instead of that of open waters. Here we conducted high-frequency surface and profiling observations of CH? and CO? concentrations in a northern site of the Poyang Lake open waters during the last summer. The study revealed significant diurnal variations in water CO? concentrations. During daytime, surface CO? concentrations were lower (15.02 μmol/L), with distinct stratification observed in vertical profiles, while nighttime surface concentrations increased (22.30 μmol/L) and vertical gradients became less pronounced. In contrast, CH? concentrations exhibited strong fluctuations without clear diurnal patterns.?CO? concentrations showed significant negative correlations (p < 0.01) with dissolved oxygen (DO), water temperature and chlorophyll content, but positively correlated with relative humidity and nitrate-nitrogen concentrations. CH? concentrations were significantly positively correlated with net radiation irradiance and inorganic carbon (DIC) concentrations (p < 0.01),?and negatively correlated with net longwave radiation (p < 0.01). A single-time sampling is always not temporally representative of daily averages, and only daytime sampling might underestimate the CO? concentration by as high as 19.9%. For the Poyang Lake, the optimal sampling time is 14–16 时 for the CH? concentration, and is 10–12 时 for the CO? concentration. This study revealed the high-frequency diurnal variation characteristics of greenhouse gas concentrations in the Poyang Lake, providing support for quantifying the uncertainties associated with key variables in the carbon cycle and for accurately estimating the lake carbon budget.