With the rapid growth of Internet-of-things (IoT) devices, IoT communication has become an increasingly crucial part of 5G wireless communication systems. The large-scale IoT devices access results in system overload and low utilization of energy efficiency under the existing network framework. In this paper, the cluster head uses the LTE-M protocol, and the intra-cluster uses the low-power wide-area network (LPWAN) self-networking protocol in the wireless sensor network. By a detailed analysis of the messages exchanged between the device and the base station, we describe the causes of overload and the steps of data aggregate combined with the physical channel. Then, we explore the cluster head quantity and the optimal scale in the intra-cluster under the traditional K-mean algorithm. When K is 30 under specific resources, the simulation results show that the system’s access success probability and resource utilization are optimal. Also, we propose a distributed dynamic cluster-head selection and clustering scheme based on an improved K-means algorithm. Simulation results show that the proposed scheme can reach 88.07% on the access success probability. The throughput and resource utilization are 3.5 times high than that of the optimal K-means.