The aim of the study was to understand the effect on the marine fishery ecosystem in waters of western Taiwan by offshore wind farms. It had two cruises of the bottom trawling, respectively in spring and autumn. We collected 72 families of biology samples, including 54 families of fish, 12 families of crustaceans, 6 families of Cephalopods. It showed that the primary species were different in the two seasons and the species. However, the seasonal clusters were not clear due to t complexity of biological species in this area. It is suggested that we need to collect the data of the marine environment, biology species, and fishery resources in the waters of western Taiwan for a long time to clarify the impact of wind farms on the fishery ecosystems.