The invention discloses an ecological catching method for small-sized mountain stream fishes. The method includes the following steps that 1, a tool is prepared; 2, site selection is conducted; 3, a stone dam is constructed; 4, a plastic film is laid; 5, transverse furrows and longitudinal furrows are dug; 6, a fishing net is placed; 7, the net is drawn; 8, a riverbed is recovered. According to the ecological catching method, the life habit that the small-sized mountain stream fishes can go upstream when the water level is lowered so as to avoid stranding is ingeniously utilized; the fish catching tool is cheap, simple and easy to obtain, mechanical operation is avoided, and no consumable items and chemicals exist, the original natural environment can be recovered quickly, and environmental protection is achieved; the fishing net is ingeniously divided into a fish catching net area and a fish containing net area, the fishes entering the net cannot escape easily, and the fishing effect is good; moreover, the size of meshes is 10 mm, juvenile fishes less than one year old can be filtered out, only adult fishes of more than one year old are caught, and regeneration of fish resources is effectively protected on the basis of rational fishing.