In order to solve the problem that the mechanism model of nonlinear system with uncertainty is difficult to establish, a modeling method of nonlinear system based on Asynchronous Fuzzy Cognitive Network (AFCN) is proposed. This method combines fuzzy cognitive network with time-lag system, and extends the node state values and weights of fuzzy cognitive network to the time interval, which enhances the adaptability of the model. At the same time an improved constrained chicken swarm optimization algorithm(ICCSOA) is proposed to identify model parameters of AFCN. A lag matrix corresponding to the actual measured values of the system lag of the nodes in the AFCN model is introduced, and a correction term including the difference between the measured values and the predicted values of the system is added to the model parameter updating mechanism. The simulation experiment results of goethite process system shows this modeling method can be used to model complex systems with uncertainties or partial missing data. The control model based on the established system model can make correct control decisions. ICCSOA has the advantages of fast convergence speed and accurate learning results, whose global search ability and convergence accuracy are higher than those of CSO algorithm, which can be widely used to the modeling of uncertain systems.