Providing security to the Mobile Ad-hoc Network (MANET) is one of the demanding and critical tasks in recent days, due to its dynamic nature. For this reason, the various routing protocols and security mechanisms are developed for the traditional networks. Nonetheless, it still lacks the limitation of increased computational complexity, inefficient security, reduced throughput, and increased delay. To solve these problems, this paper developed a new system, namely, Secure Cryptography based Clustering Mechanism (SCCM) for MANET. It comprised the following stages: secure routing, encryption, signature generation, signature verification, and decryption. After forming the network, the connection between the mobile nodes was formed. After that, the secured routing was created between the source and destination by implementing the AOMDV routing protocol. Then, the original packet was converted into an unknown format by employing an Elliptic Curve Cryptography (ECC) encryption mechanism. Consequently, the signature for the encrypted packet was generated and forwarded to the destination via the Region Head (RH) and other gateway nodes. When the destination node received the packet, it performed the signature verification process for verifying whether the packet is valid or invalid. If it were valid, the receiver would accept the data and decrypt it by using the ECC decryption mechanism; otherwise, it would reject the packet and report to the base station. The simulation results evaluated the performance of the proposed security mechanism by using various measures and compared it with other techniques for proving the superiority.