A code-based cryptosystem can resist quantum-computing attacks. However, an original system based on the Goppa code has a large key size, which makes it unpractical in embedded devices with limited sources. Many special error-correcting codes have recently been developed to reduce the key size, and yet these systems are easily broken through side channel attacks, particularly differential power analysis (DPA) attacks, when they are applied to hardware devices. To address this problem, a higher-order masking scheme for a McEliece cryptosystem based on the quasi-dyadic moderate density parity check (QD-MDPC) code has been proposed. The proposed scheme has a small key size and is able to resist DPA attacks. In this paper, a novel McEliece cryptosystem based on the QD-MDPC code is demonstrated. The key size of this novel cryptosystem is reduced by 78 times, which meets the requirements of embedded devices. Further, based on the novel cryptosystem, a higher-order masking scheme was developed by constructing an extension Ishai-Sahai-Wagne (ISW) masking scheme. The authenticity and integrity analysis verify that the proposed scheme has higher security than conventional approaches. Finally, a side channel attack experiment was also conducted to verify that the novel masking system is able to defend against high-order DPA attacks on hardware devices. Based on the experimental validation, it can be concluded that the proposed higher-order masking scheme can be applied as an advanced protection solution for devices with limited resources.