Abstract: Knowledge of the vulnerability of different species and size groups to various types of fishing methods is vital to the development of optimal harvesting strategies and rational exploitation of fish resources. In this study, the selectivity of four types of fishing methods (weir nets, gill nets, electrofishing, and cormorants) used simultaneously in a typical multi-species shallow lake (Lake Niushan, China) within the Yangtze River basin, was compared for catch composition, efficiency, and size selection. Species selectivity was evaluated with the index of relative importance (IRI). Potential fishing effects on the trophic structure of fish community were analyzed by calculating the mean trophic level (MTL) of the catches and the weight ratio between prey and predator fishes. Results indicated that the use of weir nets and electrofishing should be reduced or eliminated, because they were relatively unselective and caught many species, including juvenile individuals. Fishing efforts of cormorants should be restricted due to their high fishing efficiency, especially on piscivorous fishes. Gill nets with appropriate mesh size are likely to be a more sustainable fishing method since they were more selective in capturing larger individuals and could balance the prey-predator relationship. We suggest shifting from single-species approaches toward multi-species management, and taking trophic interactions into account to better manage fishery resources.