The characteristic water level is an important basis for flood control and early warning decision-making. In recent years, large-scale and long-lasting water level over-alarms have frequently occurred at the Sanhejian Water Level Station of the Huaihe River. The existing characteristic water level has gradually been unable to meet the needs of current flood control work. This paper uses upstream and downstream water surface line analysis, hydraulics method, water level process line comparison analysis, and highest water level annual frequency analysis to obtain the corresponding characteristic water levels, comprehensively considering factors such as the superelevation of the embankment, the principle of determining the characteristic water level, and the linkage of flood fighting and emergency rescue. A more reasonable and feasible characteristic water level is put forward. Finally, the impact analysis of the flooding situation on both banks of Sanhejian and the upstream polder area is carried out. The results show that the characteristic water level adjustment has little effect on the dikes along the banks of Sanhejian and the upstream polder; the original warning water level and guaranteed water level of the Sanhejian Water Level Station is too low and should be appropriately raised.