SummaryWireless sensor networks (WSN) are innately resource restrained and beneficial in a wide range of applications, including smart homes, e‐health care, law, military systems, disaster management, and emergency reprieve. These applications are linked to various devices that may communicate with one another through the internet, typically known as Internet of Things (IoT). The application of WSN plays an integral role in the IoT infrastructure. In a WSN, sensors are haphazardly placed in environments where the data transmission is challenged by privacy concerns. This paper proposes a methodology termed Lie hypergraph and chaos‐based secure routing (LH‐CSR) to perform an energy‐efficient routing with secure data transmission in WSN. In the first phase, the deployed sensor nodes are transformed into a hypergraph from which cluster head (CH) is elected by hypergraph transversal property, and for secure routing, the route is formed by the Lie commutators of the Lie algebra of upper triangular matrices. The second phase emphasizes privacy preservation by introducing the novel chaotic map formulation to process the key generation. The encryption and decryption processes are maintained by key generation to prevent data loss during retrieval. In this way, the data are retained confidentially with minimal computational overhead. The performance of the LH‐CSR is evaluated through a simulation, which shows that it outperforms over compared protocols in terms of cryptographic time, network lifetime, packet delivery ratio, end‐to‐end delay, and throughput.