We consider the problem of optimal control for a kind of uncertain networked systems which are composed of some heteromorphic subsystems in this paper. For the trouble of encountering the complex structure, the unavoidable uncertainties and/or disturbances of networked systems, we try to remove or eliminate the interconnected parts, uncertainties and disturbances from the system by using the method based on the stripping principle. So we can translate the control problem of uncertain networked systems into that of decentralized control. And then we use optimal control method for the remainder parts of the subsystems respectively. It is the certain kind of optimization in the rejection of uncertainties or disturbances and the optimal control for the remaining parts that we can implement the optimal control for the whole of uncertain networked systems. The theoretical analysis and simulation results are provided to indicate the effectiveness of the proposed approach.