With the rapid urbanization during the past three decades in China, the urban expressway network has arisen with large numbers in many cities. However, the traffic conditions are becoming worse and worse. One of the main reasons is that the connected sections of main road and expressway do not have a coordination by the intersection signal and variable speed limits (VSL) on expressway. In this paper, a new cooperation optimization model of VSL on urban expressway and the intersection signal timing are proposed based on the mesoscopic traffic flow model. Its objective is to minimize the total delay and the number of parking. Its essence is adjusting traffic flow on the network in space-time so that the whole network can be in a state of equilibrium. It is effective to the control of local traffic congestion and can avoid the spread of congestion, thus improving traffic safety. Additionally, the optimal VSL strategy is proposed. And then a solution algorithm based on the simultaneous perturbation stochastic approximation (SPSA) is designed for the proposed model. In the end, a practical example of Yanshan overpass in Ji’nan elevated expressway is used to validate the effectiveness of the proposed method. The simulation results are satisfactory. The conclusions are very useful for traffic management department to implement reasonable traffic control strategy.