A total of 43,417 individual of large crustacean belonging to 12 families and 40 taxa was collected. Four most dominant taxa were Metapenaeopis barbata (63.9%), Portunus argentatus (8.5%), Portunus gracilimanus (5.7%) and Stomatopoda interupta (4.2%). The CPUE ranged from 114 to 10,903 (inds./h) that the maximum occurred in December 2007 and the minimum occurred in April 2008. The monthly indexes diversity were between 0.328 and 0.732 and the average was 0.500 ± 0.120. The evenness were between 0.929 and 1.821 and the average was 1.413 ± 0.330. In addition, ecology utilization ratio EUE value was 0.758, and the weight of discarded fish accounted for 24.2% of total caught. In conclusion, in southeastern waters of Penghu, there was no significant difference in the crustacean group structure between time and space factors. Beside, in southeastern waters of Penghu, ABC curve of the observed station showed that abundance was above on biomass. The study suggested that the bottom trawling had great stress on the ecology of southeastern waters of Penghu.