Universal quantum computers are far from achieving practical applications. The D-Wave quantum computer is initially designed for combinatorial optimizations. Therefore, exploring the potential applications of the D-Wave device in the field of cryptography is of great importance. First, although we optimize the general quantum Hamiltonian on the basis of the structure of the multiplication table (factor up to 1 005 973), this study attempts to explore the simplification of Hamiltonian derived from the binary structure of the integers to be factored. A simple factorization on 143 with four qubits is provided to verify the potential of further advancing the integer-factoring ability of the D-Wave device. Second, by using the quantum computing cryptography based on the D-Wave 2000Q system, this research further constructs a simple version of quantum-classical computing architecture and a Quantum-Inspired Simulated Annealing (QISA) framework. Good functions and a high-performance platform are introduced, and additional balanced Boolean functions with high nonlinearity and optimal algebraic immunity can be found. Further comparison between QISA and Quantum Annealing (QA) on six-variable bent functions not only shows the potential speedup of QA, but also suggests the potential of architecture to be a scalable way of D-Wave annealer toward a practical cryptography design.