Intelligent devices and equipment have affected almost all aspects of our life and behavior. The type of connection and the manner of communication between this large volume of devices has caused the emergence of a vast field in the Internet called the Internet of Things, which significantly highlights the issue of energy management and increases the lifetime of networks. Complex communications, especially in mobile networks, have generated many challenges for network designers. To solve these challenges, the Software Defined Networking (SDN) paradigm has reduced the overhead in the devices caused by processing and computing by adding new capabilities to mobile IoT networks. This technique transfers energy-consuming tasks to the central controller, which manages continuous topological changes of the network in dynamic environments. This paper presents a new routing approach called Intelligent Energy-aware Routing Protocol in Mobile IoT Networks based on SDN (IERMIoT), which tries to manage the dynamic changes of topology due to the movement of mobile nodes to increase the network’s lifetime and prevent energy dissipation. For this purpose, it defines clusters of nodes and uses an intelligent evolutionary algorithm to determine the number of clusters required in the network and their balanced distribution in the dynamic environment. Also, this approach considers a mechanism to reduce the overhead of control packets and routing packets, which significantly affects the energy consumption of nodes. The simulation results indicate the proposed solution’s effectiveness compared to other simulated approaches with respect to packet delivery rate, average energy consumption, network lifetime, number of alive nodes, coverage, and routing overhead.