Danjiangkou Reservoir is the water source for the Middle Route of South-to-North Water Transfer Project. The project has been running safely and steadily since it was put into operation. However, due to the large area and wide scope of Danjiangkou Reservoir’s water source area, which involves Shaanxi, Henan and Hubei provinces, there are still some urgent management problems needed to be solved. Such problems include:(1)Management of the reservoir is weak. For example, management facilities are insufficient, funding for the protection and management lacks regular implementation, and difficulties for management of large-scale fluctuation zones after dam heightening and periodic dispatching are still challenging. (2) Water quality of some tributaries still has not reached standards and the loads of total nitrogen from tributaries are as high as 2~10 mg/L. For instance,the Shending River and Sihe River were polluted seriously, and the water quality ranked class-Ⅴ or even inferior class-Ⅴ from 2017 to 2018. (3) The system and mechanism for reservoir protection and management are still unclear, and the relevant laws and regulations are unsatisfactory. To tackle these prominent problems, we propose to build necessary management facilities, increase protection and management funding. We also put forward the standardized protection and utilization mode of water-level-fluctuation zone, clarify the supervision and management measures for water quality improvement for tributaries, and give some measures for reducing the total nitrogen load. We recommend to formulate and promulgate relevant laws and regulations, such as the Protection and Management Regulations for the Water Source Areas of the Middle Route of South-to-North Water Transfer Project as soon as possible.