An Improvement of channel structure for sound fish habitat suitability enhancement is investigated. The restoration target species of Zacco Koreanus which is represented a sound aquatic ecosystem is selected by investigating results of the fish fauna and the river environments. The changes of lower channel width for enhancing suitability indices for water velocity and depth result in habitat suitability enhancement in general by PHABSIM simulation. The habitat suitability enhancement is not guaranteed consistently by the changes of lower channel is confirmed. The optimal lower channel widths at each reach are presented by genetic algorithm of optimization which is considering the enhancement of suitability indices for water velocity and depth with given instream flows. The suggested plan of the lower channel modification will contribute to the various projects for the environmental improvement of aquatic system.