To supply better assistant decisions for military personnel with commanding activity, an analysis method for operational system command efficiency is put forward. First, built the operational system network model based on the complex network theory. And the network model was made up of logic command network and physical communication network. Then the interdependent relationship between two networks was described based on the interdependent network theory. By analyzing operational process relation among command node, firepower node, reconnoiter node, and communication node, ascertained evaluation index and calculation method of evaluation operational system command efficiency. Carried out analysis for evaluation index by simulation calculation test. The analysis result indicates this modeling method and evaluating index has an actual applying value and direction meaning for understanding and analyzing complex operational system.