Reservoir operations changed the river hydrological regimes, thus significantly altered the spatial distributions of species habitats. This research developed a fuzzy logic habitat model and combined it with a water quality model to investigate the impacts of reservoir operations on fish habitats, in particular during different life-stages. Ecologist′s knowledge was involved in this model to link environmental conditions to the quantitative Habitat Suitable Index of aquatic species. Moreover,Habitat Suitable Width Index was introduced to quantitatively characterize habitat continuity and analyze the validity of habitat variation. The model was applied to a compound channel of the Lijiang River, and simulated the habitat variations of the special fish Spinibarbus hollandi for different reservoir operation schemes in three typical hydrological years. The results indicated that water recharge from the reservoir in dry season significantly improved the suitability for fish spawning, in particular for wet and dry years that the high suitability area was increased about 50%. The water recharge had relatively small effects for fish overwintering, and the increase was only 5% in average.