This study examined the effects of the configuration of wood structures on the use of local autumn and winter habitats by fish in a remeandering reach of a large lowland river. Fish diversity was higher at the simple wood-structure (SWS) and the log-jam (LJ) sites than at the no-wood (NW) sites during both seasons. In particular, the diversity at the LJ sites was higher than that at the SWS sites during the winter. The abundance of the four dominant fish species was generally higher at the LJ sites than at the NW sites during both seasons. The SWS and LJ sites were characterized by greater depths, finer bed materials, and more diverse flow conditions during the autumn. During the winter, the LJ sites were characterized by slower currents and finer bed materials. These habitat features satisfied the various habitat requirements of the fish observed in our study reach; during the autumn, areas with fast and slow currents were favorable for juvenile salmon, silt and sand bed materials for lamprey, and deep areas for one species of goby, while slow currents were critical in the winter for abovementioned fish species. Engineered log jams were also effective in supporting the colonization of fish during both seasons. These findings suggest that a larger and more complex wood structure, particularly log jams, plays important roles in creating local habitats suitable for various fish species during the autumn and winter and in preserving fish abundance and diversity in large lowland rivers.