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Rice-wheat rotation farmland is a typical type of farmland understory in China, and its simulation effect has important reference value for climate modelling of agricultural fields in our country. The results of mesoscale climate simulation are highly sensitive to the calculation schemes of surface fluxes, and selecting appropriate flux calculation schemes is crucial for simulation accuracy. Therefore, it is of great significance to compare and analyse different flux calculation schemes under the rice-wheat crop rotation system. In this paper, eight representative near-surface turbulent flux calculation schemes are selected, and the measured data from the Shouxian National Climatological Observatory are used to compare and analyse the calculation characteristics and differences of the schemes in the underlay of rice-wheat rotation farmland using the method of normalised standard deviation. The results show that the error characteristics of the schemes are different under different stabilised stratification conditions and wind speed conditions. In general, the overall average normalised mean difference of momentum flux of all schemes is 0.536, of which the maximum is 0.575 for the Sharan and Srivastava, 2014 scheme (SS14 scheme) and the minimum is 0.517 for the Sharan and Srivastava et al., 2020 scheme; and the overall average normalised standard deviation of sensible heat flux of all schemes is 0.638, of which the maximum is 0.871 for the Gryanik et al., 2020 scheme and the minimum is 0.476 for the SS14 scheme. In addition, this study is also giving the error characteristics of each flux calculation scheme under different stratification conditions and wind speed conditions under the rice-wheat rotation farmland, and finally, this paper is giving recommendations for the selection of turbulent flux calculation schemes for the rice-wheat rotation farmland, for the momentum fluxes, under the unstable stratification conditions, it is recommended to use the SS14 or Li et al., 2014 & 2015 schemes (Li1415 scheme), the Businger, 1971 scheme is recommended for weakly stabilised stratification, and Wang et al., 2002 scheme (Wa02 scheme) is recommended for strongly stabilised stratification; for heat flux calculation, Li et al., 2010 scheme (Li10 scheme) is recommended for unstable and weakly stabilised stratification and Li1415 scheme is recommended for strongly stabilised stratification. Under low wind conditions, it is recommended to use SS14 or Li1415 scheme to calculate the momentum flux and Li10 scheme to calculate the sensible heat flux; under strong wind conditions, it is recommended to use Li1415 scheme to calculate the momentum flux and Gryanik and Lüpkes, 2018 scheme or Wa02 scheme to calculate the sensible heat flux. These findings of this paper support the accurate calculation of near-surface layer turbulent flux.