Eco-morphological diversification is often associated with functional changes that adapt well to different niches. However, the patterns of adaptive variation can vary depending on ecological niche conditions. The population of a bottom dwelling fish, Pseudogobio esocinus, exhibits continuous mouthpart variation linked with the individual diets even within a single site in Lake Biwa. Lake individuals mostly utilize chironomids (buried in the bottom) as prey, but the narrower-mouthed fish use a higher proportion of amphipods (moving on the bottom). To examine feeding adaptation in this fish population, we tested the relationship between mouthpart variation and feeding performance through aquarium experiment, and observed mechanistic changes in mouth movement related to different feeding styles. The narrower-mouthed fish showed higher utilization of amphipods and more frequent attacks with active movement than the wider-mouthed fish. Such narrow mouths, linked with more forward mouth protrusion, may be advantageous for picking up moving prey in the water column. These results imply that fish with narrower mouths not only prefer amphipods, but also have higher attack rates on them by changing attack behavior depending on their phenotypes. We discuss the feeding adaptation and its related function for the different mouth types within a population.