Abstract: In order to understand the characteristics of trophic structure of main fishery in typical gulf of southern China with significant habitat difference, we analyzed the ratio of carbon and nitrogen stable isotopes (δ¹³C and δ¹⁵N) of major fishery species collected in Hailing Bay and Lingshui Bay in wet season of 2015, and calculated several quantitative metrics based on the δ¹³C and δ¹⁵N ratios so as to quantitatively characterize the trophic structure in community-wide aspect. The results show that the average δ¹³C −15.36±0.62)‰ and δ¹⁵N (15.53±0.94)‰ values of main fishery species in Hailing Bay were significantly higher than those in Lingshui Bay (−17.44±1.21)‰ and (13.78±1.31)‰, P<0.01. However,  the NR and TA values of Hailing Bay were lower than those of Lingshui Bay, showing longer food chain length and higher diversity in Lingshui Bay. Calculated by 3.4‰ as a nutrient grade of nitrogen stabilized isotope enrichment, the grade distance of Lingshui Bay fishery was only 1.37, lower than 1 of Hailing Bay, indicating that both Lingshui Bay and Hailing Bay have relatively less high trophic organisms and the food webs are often disturbed.