Secured communication over the Wireless Sensor Network (WSN) is one of the prime concerns nowadays as the wireless communication medium suffers under a wide range of networks. For establishing secured communication over WSN, literature has suggested the key level management protocol, where each transmission is established based on the availability of secured key. This work develops a key management protocol, namely Multi stage key management (MSKM) protocol, for the secured communication over the clustered WSN. The entire protocol is implemented in three stages, such as pre-deployment, key generation, and key authentication and verification. In the first stage, the nodes are provided with the identity, and then, the second stage uses the homomorphic encryption model, for generating the necessary key to the communication. Finally, a mathematical model is developed in this work with several factors, such as a hashing function, homomorphic encryption, dynamic passwords, profile sequence, random number, and EX-OR functions. The proposed MSKM protocol establishes the secured communication over the WSN by authenticating the entities. The entire work is compared with several states of art techniques and evaluated based on several metrics. The proposed MSKM protocol achieved values of 0.122 kb, 0.929, 2.332 kb, and 14.586 joules for the communication overhead, detection accuracy, key memory storage, and energy, respectively.