AbstractThe flux calculation schemes (FCSs) and gas sampling schemes (GSSs) determine the accuracy and representativeness of non‐steady‐state chamber measurements. The study aimed to provide guidelines on FCSs and GSSs to improve cumulative flux estimations of the non‐steady‐state chamber method. Based on a dataset obtained from automated chamber measurements in a permafrost‐affected wetland in northeast China, we evaluated the effects of FCSs and GSSs on cumulative methane and nitrous oxide flux estimates at the field scale. The evolution of chamber headspace gas concentrations was classified into five patterns, presenting the measurement disturbance and variation of non‐steady‐state chamber method. Three FCSs, that is, the sole use of linear model and hybrid use of linear with empirical quadratic and theoretical exponential models, were established on the basis of evolution patterns of chamber headspace gas concentrations. The hybrid FCSs were more robust for cumulative flux estimates than the sole FCS of the linear model. The flux dataset with the high spatiotemporal resolution was subsampled to simulate datasets obtained with different GSSs. The subsampling of flux dataset proved optimization of GSSs by allocating limited measurement resources to preferentially promote the spatial representativeness of measurements (e.g., with more replicate chambers and stratified chamber placement according to microtopographies), characterize the small‐scale spatiotemporal variability of fluxes (e.g., diurnal variation and spatial heterogeneity due to microtopographies), and capture the evolution pattern of chamber headspace gas concentrations, could effectively improve cumulative flux estimates at the field scale. Our guidelines on FCSs and GSSs can serve to the improvement of non‐steady‐state chamber methodology.