In heterogeneous environments, the Internet of Things (IoT) combined with mobile ad hoc network (MANET), i.e., MANET-IoT network, becomes more attractive to end users and economically successful. However, the introduction of MANET potentially makes the system more prone to attacks due to its lack of centralized management, weak connectivity, and resource constraints. To enhance the network robustness to intentional attacks, the critical nodes of the MANET-IoT network should be firstly identified and then protected. Most of the existing methods for identifying critical nodes usually focus on static networks or a single topology snapshot in dynamic networks without considering the correlation between topology snapshots, which cannot effectively deal with the dynamic changes in the topology of MANET-IoT networks. In this paper, a dynamic critical node identification (DCNI) method is proposed. First, we propose a comprehensive metric to measure the node importance in the topology snapshot. Then, we introduce a sliding time window to filter out the topology snapshots which have a close correlation with the current snapshot, and fuse the importance values of the same node in different topology snapshots. Finally, the critical nodes are selected based on the ranking result of fused importance. Thereafter, the port hopping mechanism could be applied to the critical nodes for enhancing network defense capability. The simulation results show that the proposed method is more effective in identifying critical nodes than existing static methods in MANET-IoT networks, and the port hopping mechanism can improve network defense significantly to denial of service (DoS) attacks.