With higher recognition on conservation of endangered species in Taiwan, one of the major conservation projects for the government is the restoration of Formosan Salmon (Oncorhynchus masu formosanum) which is threatened by check dams in the channels for blockading the pathway to upstream and causing the problems of population isolation and close-blood mating for this treasure fish. Auxiliary fishways were investigated and installed to solve this problem, but their effect was decreased dramatically by the damage and deposit of sediment. By partially breaking the dam body or cutting opening appropriately, this study tried to provide alternative solution for this problem through model experiments. Based on the experiment results, this method of habitat improvement does not have serious impacts on channel stability and sedimentation. The best alternative from various combinations of opening types and destruction procedures for check dam #4 of Chi-Chia-Wan Creek is to convert the original dam into detention dam with trapezoid opening based on the considerations of upstream channel slope increment, scoring depth, flush flute formation, and downstream sedimentation increments on discharge and concentration. Besides, this study suggests that the best operation time for habitat improvement is between March and April before raining season according to hydrologic records and the characteristics of Formosan Salmon.