This research was conducted from April 2008 to March 2009 in the southeastern waters of Penghu. Data for qualitative and quantitative analysis were collected by trawlers. After the species were identified, the diversity index, evenness, similarities, cluster, ordination, ecological use efficiency, environmental factor and method of interference were used to evaluate species composition and community structure characteristic. A total of 32,787 individuals of fish belonging to 63 families and 121 taxa was collected. The five most dominant taxa were Leiognathus rivulatus (42.8%), Acropoma japonicum (21.5%),Upeneus japonicus (15.7%), Saurida elongata (4.7%), and Diodon holocanthus (10.6%). The CPUE ranged from 13.4 to 55.3 (kg/h) with the maximum occurring in September 2008 and the minimum occurred in October 2008. The monthly diversity indexes were between 0.650 and 2.247, and the average was 1.552 ± 0.631. The evenness values ranged between 0.180 and 0.618 with an average of 0.423 ± 0.165. The estimated ecology utilization efficiency was 0.520, and the weight of discarded fish accounted for 47.9% of the total catch. In conclusion, in the southeastern waters of Penghu, there were no significant differences in the fish group structure for time and space factors. In addition, the ABC curve of the observed station showed that abundance was over biomass. The study suggested that the bottom trawling operation had caused a great stress on the fishing ground.