The Pearl River estuary is the second largest estuary in the South China Sea. The species composition and trophic structure of shrimp-trawl catches from this estuary were investigated using stable isotope analyses during the winter of 2012. Crabs dominated the catches, constituting 37% of the total biomass in the inner estuary and 45% in the outer estuary. The δ15N and δ13C values for particulate organic matter gradually changed from the inner to the outer estuary. δ15N of particulate organic matter was more enriched in the inner estuary, while δ13C was more enriched in the outer estuary. Higher δ15N values in the inner estuary suggested a stronger influence from anthropogenic eutrophication. The δ15N and δ13C values of shrimp-trawl catches showed the same trends as the particulate organic matter. Trophic structure and faunal composition of shrimp-trawl catches varied greatly between the inner and outer estuary areas. The trophic niches were clearly distinct among fishery groups in the outer estuary. Community-wide metrics of stable isotope values showed that there was greater diversity of food sources and more complex trophic interactions in the inner estuary, whereas trophic levels were more evenly distributed in the outer estuary.