In Internet of Things (IoT) applications with multihop networking, not only traditional energy efficiency but also many distinct features should be considered when designing routing protocols, including different security requirements, heterogeneity, and scalability. In this article, an energy-efficient multilevel secure routing (EEMSR) protocol in IoT networks is proposed. Considering that clustering is a reasonable solution of conserving energy, a cluster-based multihop routing protocol is utilized to reduce the high communication overhead due to the scalability of IoT networks. In particular, more reasonable analytic hierarchy process and genetic algorithms are adopted to assign accurate weight and optimize intercluster routing in which heterogeneous IoT networks are considered to support large amount of heterogeneous IoT entities and services. Moreover, multiple trust levels are adopted to defend the different attacks by calculating the trust factor on the clustering and routing, including data perception trust, data fusion trust, and communication trust. It is shown that the proposed algorithm outperforms the existing algorithms in terms of network lifetime, throughput, packet delivery ratio, network energy balance, and adaptability.