By using Ecopath with Ecosim 5.1 software, the Ecosim model of Beibu Gulf marine ecosystem in 1959-1960 was constructed, which included about 20 functional groups such as fishery, marine mammals, sea-birds, sharks, pelagic fishes, demersal fishes, and benthic crustaceans, etc. Through the comparison with the investigation data in 1997-1999, the effects of fishing on the structure and function of Beibu Gulf marine ecosystem were analyzed. The results indicated that with the increasing fishing pressure in past forty years, the ecosystem structure and function shifted drastically, with the biomass of long-lived, high trophic level and piscivorous fishes declined while short-lived and small fishes and benthic invertebrates dominated gradually. The biomass of piscivorous species in 1999 was only 6% of that in 1960, while cephalopods increased 2.7 times or more. The trophic level of the catch declined from 3.2 in 1960 to 2.98 in 1999, which fitted the rule of "fishing down the food web" and suggested that the present exploitation patterns were unsustainable. Based on the data of the 1990s, the changes of the ecosystem under decreasing fishing pressure were predicted. This study validated the feasibility of Ecosim model in predicting the effects of fishing pressure on marine ecosystem.