Abstract: Now is a critical period of the red lines for ecological protection that from the policy to law. It is urgent to study deeply the internal mechanism and the legalization path of the red lines for ecological protection especially under the background of the new era. It also provides the decision-making basis for the ecological civilization system reforming, thereby to ensuring the national and regional ecological security. The red lines for ecological protection is guided by the comprehensive ecosystem method theory and is the specific application of the theory. It is mainly embodied in the ecological spatial planning management degree, the ecological space classification and classification control system and the effectiveness evaluation system. From the perspective of the overall of the ecosystem, the spatial control of the ecological space planning should be established in a unified framework, which is include the relevant departments to supervise and implement of the natural resources, to distribute and adjust the benefits. According to the flexibility analysis of the ecosystem management method, it adopts the policy of establishing a classification control system through the adaptive management and mitigation measures which is based on the flexibility of the ecological space and the carrying capacity. On the opinion of analysis the dynamism of the ecosystems, the structure and function of ecosystems change with time. Setting up an effective evaluation mechanism must consider the impacts of the short and long-term ecosystem structure and function.