Natural protected areas system planning is a special planning in the “five levels and three categories” of national territory spatial planning system. The study analyzes the practical problems of the construction of nature protected areas system and the objective needs of the overall compilation of “nature protected areas system planning”, clarifies the connotation and extension of “nature protected areas system planning”, and puts forward the characteristics of “nature protected areas system planning” and the compilation points at all levels under the “conduction” framework based on the classification of national territory spatial planning system. It is of practical significance to the construction and reform of China’s nature protected areas system and mechanism, and plays an important supporting role in the discussion of special planning of land space planning system.