Based on the tidal flow mathematical model and erosion-deposition prediction model, we analyze the flow field variation and waterway siltation density to explore the effects under different ratios of length to width and implementation schemes for the borrow area in the shoal of Taizhou bay. It is shown that the variation amplitude of the flow field and waterway siltation density is relatively large on the engineering area after the borrow area is excavated, and that decreases significantly in the region 3km outside the borrow area. Under the condition of certain volume of the borrow area, the ratios of length to width and length to depth are smaller, and the amplitude of flow field variation and waterway siltation density is smaller. Compared with the full excavation schemes, the amplitude of the waterway siltation density can be reduced about 30% by the segmental excavation schemes. This research result may serve as reference for the planning and design of the borrow area.