Based on the MIKE21-Flow model, a two-dimensional flow mathematical model has been established to study the characteristics of motion of a stagnation point under different runoffs and tides in the Oujiang River estuary. And based on historical data, this paper analyzes the dynamic effect of the stagnation point migration on the entrance bar. The research results demonstrate that due to the changes of flow conditions, the location of the stagnation point will make appropriate response. And this unique characteristic of motion is in conformity with the evolution of the entrance bar. When river discharge decreases, the stagnation point moves upstream so actively that a dynamic balance zone is formed at both south and north branches, and scouring at the entrance bar occurs. When river discharge increases, affected by the split ratio and the riverbed topography, the stagnation point moves towards downstream with different extensions at the south and north branches, which makes the entrance bar have further deposition. The research results have a great significance in understanding the hydrodynamic changes in the Oujiang River estuary under the influence of the existing works.