Abstract: In this paper the hypothsis prerequisite for resource optimal allocation under market economy structure and the basic concept of ineffective market are analysed,and the principles that government intervention should obey and the reasons that arouse inactive intervention are also presented,Then the author discussed the features of natural resources as public goods and the necessity and complexity in protection,utilization and exploitation of natural resources according to its characteristics and market principles.Furtherly the concept,structure,process system,logical system,and knowledge system of the systems engineering for natural resource management are expounded,and the methods for analysis of the benefit cost is introduced.