Abstract: Based on the investigation data of gillnets of three different structrues (single wall, double wall, trammel gillnet) of different mesh sizes (40mm, 50mm, 60mm) in the Pearl River Estuary coastal waters in September of 2014, we analyzed the resources community structure of gillnet fishery. The results indicate that the species number, total number and weight of the three kinds of gillnets decreased with increasing mesh size. The species with index of relative importance (IRI) above 1 000 were defined as dominant species, but Nemipterus bathybius was the same dominant species. Since the fish body size varied remarkably, we calculated Margalef richness index, Shannon-Wiener index, Simpson index and Pielou evenness index based on individual number and biomass. T test shows significant difference among diversity indices. The Euclidian distance shows significant difference in community structure of gillnet fishery of different mesh sizes, but no significant difference was found in the same mesh size. Thus, controlling appropriate mesh size is currently the most effective measure to increase fish diversity and resume the stabilization of ecosystem.