Feedback-controlled electromigration (FCE) is employed to control metal nanowires with quantized conductance and create nanogaps and atomic junctions. In the FCE method, the experimental parameters are commonly selected based on experience. However, optimization of the parameters by way of tuning is intractable because of the impossibility of attempting all different combinations systematically. Therefore, we propose the use of the Ising spin model to optimize the FCE parameters, because this approach can search for a global optimum in a multidimensional solution space within a short calculation time. The FCE parameters were determined by using the energy convergence properties of the Ising spin model. We tested these parameters in actual FCE experiments, and we demonstrated that the Ising spin model could improve the controllability of the quantized conductance in atomic junctions. This result implies that the proposed method is an effective tool for the optimization of the FCE process in which an intelligent machine can conduct the research instead of humans.