The fluctuating backwater zone navigation flow conditions of Shatuo hub are affected by both the upstream Silin hub daily regulation and downstream Shatuo reservoir scheduling. Based on the 2D flow mathematical model of the two dams, this paper studies the fluctuating backwater zone regulation scheme and presents a scheme optimization. The results show that after implementation of waterway regulation, the shoal reach channel of the fluctuating backwater zone reaches grade IV standard, which provides technical reference for waterway regulation scheme design.