Some uncertain problems in the element level cooperative control of distributed combat system are analyzed, including the applicability of consistency theory to the element level cooperative control of distributed combat system, man in the loop and autonomous cooperative control. The three-layer complex nonlinear dynamics model with perception, decision-making, and engagement is described，which using algebraic graphic, dynamics and automatic control theories. Furthermore, the order parametric model of element level autonomous cooperation, which in order to measure the cooperation ability and performance of the distributed combat system are researched.