This paper presents an initialization method that can approximate a given approximate Ising model with a high degree of accuracy using the Factorization Machine (FM), a machine learning model. The construction of Ising models using FM is applied to the combinatorial optimization problem using the factorization machine with quantum annealing. It is anticipated that the optimization performance of FMQA will be enhanced through the implementation of the warm-start method. Nevertheless, the optimal initialization method for leveraging the warm-start approach in FMQA remains undetermined. Consequently, the present study compares a number of initialization methods and identifies the most appropriate for use with a warm-start in FMQA through numerical experimentation. Furthermore, the properties of the proposed FM initialization method are analyzed using random matrix theory, demonstrating that the approximation accuracy of the proposed method is not significantly influenced by the specific Ising model under consideration. The findings of this study will facilitate the advancement of combinatorial optimization problem-solving through the use of Ising machines.