The stage-discharge relationship is an important basis for estimating water surface line. Using the Manning formula directly to calculate the relationship of water level and flow will produce great errors, and the unreasonable phenomenon is that the decrease of flow with the increase of water depth will occur when flood is out of bank. In this paper, the transverse distribution of the average vertical velocity and the monotonicity of the flow-depth function of the Manning formula are first analyzed, and then the reasons for such errors and unreasonable phenomena are discussed. In addition, the calculation accuracy of different methods such as horizontal segmentation, vertical segmentation, diagonal segmentation, wetted perimeter correction, weight segmentation, Xie Hanxiang method and synergism method is compared to demonstrate the applicability of the improved Manning formula in the compound channel. The results show that the velocity difference between the main channel and the floodplain makes the flow move laterally, which will lead to produce a large amount of momentum exchange at the junction, and its mechanism of action is completely different from the single channel, so the Manning formula cannot be applied directly to the compound channel. When the growth rate of hydraulic radius and the wetted perimeter satisfy a certain condition, the flow-depth function is monotonically decreasing, and the flow decreases with the increase of water depth. Compared with the results of different calculation methods, it is found that the precision of wetted perimeter correction is the lowest and not recommended. The precision of horizontal segmentation, vertical segmentation, diagonal segmentation and weight segmentation is close to the traditional theoretical method, so the improved Manning formula can be better applied to the compound channel. Diagonal segmentation is recommended in this paper because the diagonal segmentation method has the highest accuracy and the most simple calculation in all the methods.