This paper presents an initialization method that can approximate a given approximate Ising model with a high degree of accuracy using a factorization machine (FM), a machine learning model. The construction of an Ising models using an FM is applied to black-box combinatorial optimization problems using factorization machine with quantum annealing (FMQA). It is anticipated that the optimization performance of FMQA will be enhanced through an 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 initialization methods based on random initialization and low-rank approximation, and then identifies a suitable one for use with warm-start in FMQA through numerical experiments. Furthermore, the properties of the initialization method by the low-rank approximation for the FM 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 advancements of research in the field of black-box combinatorial optimization through the use of Ising machines.