Despite a wide variety of secured authentication schemes is available for to address the issues in Cyber Physical System (CPS) problems, their security is assured only up to some extent. A novel Hypergraph (HG) based hashing technique to have a secure authentication between the IOT edge devices in any Cyber Physical System/Internet of Things environment which can be used between pairs of edges devices is proposed, which is based on the authentication scheme between the edge devices that can achieve informal verification, prevent key escrow problem and also save from various attacks such as perfect forward secrecy attack, impersonation attack, man-in-the-middle attack. The security analysis of proposed HG authentication scheme has been validated by means of formal verification using AVISPA tool and ROR model. Also, the proposed protocol has been compared with the existing protocol and it provides a high resistance of attacks, low computation and communication cost. Comparative security analysis with recently reported techniques shows that the proposed scheme is superior to many techniques in terms of communication and computational costs. The key findings include the capability of HG in strengthening hashing function during authentication and provides better security when compared to existing ones.