The present authors recently developed a time-dependent Ginzburg-Landau (TDGL) formulation for ordering processes of B2 and D03 in binary alloys, taking into account the symmetrical relationships between these ordered phases. Kinetic equations for time-evolution of order parameters and the composition one are derived from the Ginzburg-Landau type potential consisting of a mean-field free energies and interfacial energy terms. On the other hand, coauthors have investigated domain structures in two-step phase separation of Fe-based Fe-Ni-Al alloys. Micro-structures in the superalloys consist of B2 ordered domains and A2 disordered matrices in the first stage of phase separation. The second stage during a subsequent aging leads to formation of B2 domains and A2 phase regions in the former A2 matrices and B2 domains, respectively. The evolution of three-dimensional domain structures and composition profiles has been analyzed by electron tomography imaging and energy-dispersive X-ray spectroscopy. In this work the authors have applied the TDGL formulation to this alloy system, and performed three-dimensional numerical simulations assuming the thermal processing. The results of the simulations well reproduced the characteristics of the micro-structures obtained from the observations.