The prevention and control of drinking water source pollution is one of the focuses of water resources, water ecology and water environment protection project of Yangtze River economic belt. Due to unclear horizontal management authority division, the absence of longitudinal end regulation and ecological compensation system, improper punishment design, and the loopholes of drinking water source water quality monitoring system and other reasons, the pollution of the Yangtze River economic belt and drinking water sources showed a trend of worsening, which were mainly manifested on local pollution turning to universality pollution, single city type pollution turning to urban rural compounded type pollution, point and non-point sources of industrial and agricultural pollution become the main sources of pollution. The solution to the current drinking water pollution prevention dilemma should conduct innovative management system, clarify the relationship between transverse and longitudinal relationship, improve the ecological compensation system for drinking water source, increase illegal costs and complete the system of water quality monitoring of drinking water source.