The northeastern waters of Guishan Island constitute one of the crucial fishing grounds for coastal trawl fishery in Taiwan and have been exploited for many decades. To construct the marine ecosystem and to examine the interactions among trophic levels of fisheries resources in the waters of Guishan Island, historical catch, catch composition, biological information, fishing effort, environmental data such as sea surface temperature, salinity, and nutrients were analyzed using Ecopath with Ecosim. The results indicated that the longline and drift net fisheries have a very minor incidental catch of cetaceans, with a fishing mortality (F) of 0.01 year−1 and an exploitation rate (E) of 0.03. The F and E were 0.308 year−1 and 0.617 for small skates and rays, and were 0.261 year−1 and 0.580, respectively, for small sharks. The F and E of the dolphinfish, Coryphaena hippurus, an important pelagic species, were 0.411 year−1 and 0.245, respectively. Fisheries had negative impact on major commercial species except the dolphinfish and the oil fish, Lepidocybium spp., which benefited from the reduction of their predators or competitors. The keystone species of the Guishan Island marine ecosystem is phytoplankton, which has the lowest trophic level and great biomass, and is an important energy source of the ecosystem. The influences of zooplankton and anchovy rank as second and third, respectively, with regard to the keystone species in the ecosystem due to their great biomass. Regarding the biomass of less abundant species, carangids had the highest influence followed by hairtail due to their feeding habits. The results of simulations using Ecosim indicated that the hairtail, small sharks, skates and rays, mackerels, and marine eels will benefit if fishing efforts are reduced by 30%. On the other hand, the biomass of phytoplankton, zooplankton, demersal benthivores, and shrimps will decrease due to the increase in the biomass of their predators.