Manyusha shoal head protection engineering is 2.2 km long and 0.58 km wide on the straight reach of Yangtze estuary, which is simulated with narrowed complete beach protection and sides’local beach protection, and through which the scour depth and position of beach protection engineering under different flow conditions are obtained. The influence of ballast at the edges of the protection works and ballast spacing on scour is studied. The ballast at the edge of protection engineering which should be widened and the key protection parts are proposed, so as to provide a reference for the design and related research.