Although Eddy Covariance (EC) technique is one of the best methods for estimating the energy and mass exchanges between underlying surface and atmosphere in micrometeorology, errors and uncertainties still exist without necessary corrections. In this paper, we will focus on the effect of coordinate system on the eddy fluxes. Based on the data observed over four sites (one farmland site, one grassland site and two forest sites), the effects of three coordinate system transforming methods (Double Rotation-DR, Triple Rotation-TR and Planar Fit-PF)on the turbulent fluxes are analyzed. It shows that (i) the corrected fluxes are more or less than the uncorrected fluxes, which is related mainly to the sloping degree of surface, wind speed and wind direction; and (ii) pitch angle has a sinusoidal dependence on wind direction, especially in the regular sloping terrain; and (iii) PF method is something like the simplification of TR or DR,and there are not obvious distinctions in correction in sloping grassland and flat farmland, but PF method is not suitable for uneven and irregular forest sites.