The Qingshan hydro-junction reconstruction project on the Lishui River is mainly to build ship locks and structures for water retaining and discharge after demolishing the original buildings on the left branch. To tackle the problems in flood discharge capacity and navigation of the hydro-junction involved in the general layout plan of the Qingshan hydro-junction reconstruction project，the paper studies the general layout and flood discharge capacity of the hydro-junction and the navigation conditions of the entrance area in the ship lock. A general physical model is adopted for tests，and a comparative analysis is carried out on the discharge capacity and navigation conditions of the current situation and the design scheme of the hydro-junction. In this way，the original design scheme is optimized. The results show that the discharge capacity of the hydro-junction is close to the current situation；when the main flow of the left branch deflects to the middle and right part，the navigation flow conditions in the entrance area of the ship lock are improved. Therefore，we recommend demolishing the original left branch buildings，moving the axis down 300 m，building a sluice with eleven holes，reducing one-hole sluices to connect the dam section，and changing the left two-hole sluice to a two-hole spillway dam. The recommended scheme is feasible，and the navigation conditions in the entrance area are significantly improved.