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Software Defined Network (SDN) is a programmable network which separates the control logic-plane and hardware data-plane. The SDN centrally manages different Internet of Things (IoT) enabled smart devices like, actuators and sensors connected in the networks. Smart city infrastructure is an application of IoT network which purpose is to manage the city network without human interventions. To collect the real time data, such smart devices generate large amount of data and increasing the traffic in network. To maintain the quality of services (QoS) of smart city IoT networks, the SDN needs to deploy the multi-controllers. But the communication performance reduces due to unbalance load distribution on controllers. To balance the traffic load of controller an intelligent cluster based Grey Wolf Optimization Affinity Propagation (GWOAP) Algorithm is proposed when deploying the multiple controllers in SDN-IoT enabled smart city networks. The proposed algorithm is simulated and the experimental results able to calculates the minimum overall communication cost in comparison with Genetic Algorithm (GA), Particle Swarm Optimization (PSO) and Affinity Propagation (AP). The proposed GWOAP better balance the IoT enabled smart switches among clusters and node equalization is balanced for each controller in deployed topology. By using the proposed methodology, the traffic load of IoT enabled devices in smart city networks intelligently better balance among controllers.