In order to optimize and improve network combat system, evaluates and analyzes the structure effectiveness of network combat system based on the theory and method of complex network. Builds the network combat system and analyzes its connotation and characteristics and then models it. Construct 4 structure effectiveness indexes accordance with the relationship between the complex network statistical parameters and the structure of the network combat system. From the perspective of complex network the paper also analyzes its structure effectiveness comparing with traditional combat system and puts forward the methods and strategies to optimize and improve its structure. The results show that network combat system structure can realize the networked flat structure, they also show the higher degree of resource sharing and coordination, the stronger the ability of feedback optimization and network combat system structure is obviously better than the traditional structure.