Abstract: The traditional methodology for pollution control usually only focuses on the point source pollution, while ignores the non-point source pollution and endogenous pollution in lake. It is necessary to change the ideas and methods urgently, and consider all kinds of pollution sources in the whole basin. Taking the whole basin as the control unit, a systemic, three dimensional and multi-level pollution control system for a basin was built up scientifically. This system pays attention both to “management” and “treatment”, which effectively covers pollution control in the whole process of the pollution sources (point and non-point sources), pollution pathways (surface runoff and river) and terminal pollution (lake endogenesis and internal load). This novel methodology should provide scientific reference for the present comprehensive control of basin water pollution.