| Optimizing and strengthening the spatial management is an important strategic task of the top-level design of economy development, resources utilization and ecology and environment protection policies in the new era. In recent years, series policies of territory development, emphasized the requirements of strengthening the construction of ecological civilization in territory development plan, and clearly put forward major adjustments, such as multi compliance, usage control, etc. As an important part of territory development specialized plans, the spatial management system of watershed ecology and environment protection needs to be adapt to the requirements come along with new territory development planning system. In this paper, the evolution process of the spatial management system of watershed ecology and environment protection is combed in detail, the requirements in new era are analyzed in depth. At last, in order to provide decision-making reference in the new ear, this paper puts forward the concept of spatial zoning system, comprehensive target index system, management measures and responsibility implementation mechanism for water eco-environment protection.