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Networked cyber-physical systems (NCPS), where control and communication are closely integrated, have been envisioned to have a large number of high-impact applications. In this paper, a joint optimization framework is presented, which combines the objective of control as well as other relevant system objectives and constraints such as communication errors, delays and the limited capabilities (e.g., energy capacities) of devices. The problem is solved by an online optimization approach, which consists of a communication protocol and a simulated annealing based control algorithm. Meanwhile, by taking into account the communication cost, we optimize the control intervals by integrating two kinds of acceptances, i.e., cyber and physical acceptances, into the control algorithm. Numerical results show the effectiveness of the proposed approach.