To clarify the backwater characteristics of bridges in the upper reaches of the Yellow River and to investigate the reliability of the numerical simulation methods in flood control calculations, seven consecutive bridges in the Qingtongxia-Shizuishan section of the Yellow River (hereinafter referred to as the “Qing-Shi section”) in the Ningxia Hui Autonomous Region were selected as the research objects to construct a two-dimensional hydrodynamic model using the MIKE21 hydrodynamic module. Then the model was applied to the numerical simulation and comparative analysis of backwater characteristics of bridges under different flood frequencies. The results show that in the calibration and verification process, the relative errors between the simulated and measured values were less than 5%, the boundary constraints and channel roughness should be determined after the calibration. The velocity of the river channel decreased with the decrease of the flood peak flow, and the backwater of the bridge-piers fluctuated in the range of 0.10-0.28 m. According to the comparative analysis of the simulation results of the model and the calculation results of the empirical formulas, the calculated results of the Henderson formula were in good agreement with the simulation results which presented consistent change trends; whereas those of Lu Hao’s formula overestimated the situation. This study can provide an empirical reference and theoretical basis for the influence analysis of backwater characteristics of river-crossing buildings and the flood control calculations of river channels.