Cryptography is the essential component in any protocols for securing the communication. Diffie and Hellman introduced the concept of Public key cryptosystem, which uses two different keys for secure communication. Ralph Merkle and Martin Hellman invented a public-key cryptosystem named as Merkle-Hellman Knapsack Cryptosystem (MHKC) which is an NP-complete combinatorial problem believed that computationally difficult to solve by intruders. All the public key elements are the modulus of multiples of super increasing sequence. Adi Shamir performs cryptanalysis and breaks the MHKC in polynomial time. In this paper, a novel public key cryptosystem based on MHKC (NPKC-MHKC) has been proposed, which is secure than MHKC. NPKC-MHKC consists of Public key, Private key, and Session key. Since all the three keys depend on each other, it is computationally infeasible for the intruder to break the cryptosystem. The performance analysis shows that the execution time of NPKC-MHKC is comparatively lesser than MHKC and security analysis proves that NPKC-MHKC is secure than MHKC. So, NPKC-MHKC can be implemented in High-performance computing applications.