To investigate inter- and intra-specific trophic relationships among dominant coral reef fishes in Qilianyu Islands of the Xisha Islands, the trophic structure characteristics of six common and dominant fish species were analyzed using carbon (δ13C) and nitrogen (δ¹⁵N) stable isotope techniques in September 2021. The results indicate that Naso lituratus had the highest δ13C and the lowest δ¹⁵N values with averages at (−10.88± 1.42)‰ and (5.74±0.37)‰, respectively. In contrast, Zanclus cornutus had the lowest δ¹³C value with an average of (−15.27±0.74‰), and Gnathodentex aureolineatus demonstrated the highest δ¹⁵N value at (9.94±0.73)‰. N. lituratus and Ctenochaetus binotatus primarily distributed in areas with high δ13C and low δ¹⁵N values, while Z. cornutus, Chaetodon auriga, G. aureolineatus, and Epinephelus merra tended to occupy areas characterized by low δ¹³C and high δ¹⁵N isotopic signatures. Mean trophic levels (TL) of N. lituratus, C. binotatus, Z. cornutus, C. auriga, G. aureolineatus, and E. merra were 2.24, 2.45, 2.89, 3.20, 3.48, and 3.02, respectively. The isotopic niche of G. aureolineatus occupied the highest position and had the largest values, with CR, NR, TA, SEA, and SEAc reaching 5.90, 3.18, 9.00, 2.09, and 2.11, respectively. Z. cornutus exhibited the smallest isotopic niche among both omnivorous and carnivorous fishes, positioned at the lowest tail. Among herbivorous fishes, the isotopic niche of N. lituratus was larger than that of C. binotatus, but remained below the latter. Overall, δ¹⁵N values of omnivorous and carnivorous fishes were larger than herbivorous fishes, and the stable isotope core niches of all fish species exhibited complete non-overlapping distributions. G. aureolineatus and E. merra might exhibit differences in spatial, temporal, and dietary ecological niches, resulting in non-overlapping core isotopic niches. N. lituratus and C. binotatus likely differed in spatial and dietary ecological strategies, leading to distinct core isotopic niches. Z. cornutus exhibited distinctive dietary differences compared to other species, resulting in non-overlapping isotopic niche with others. Lastly, C. auriga, characterized by strong territorial behavior and diverse food sources, suggesting niche separation from other fishes primarily through spatial and dietary divergences. Strong positive correlations between standard length and δ¹⁵N were observed in all species except Z. cornutus (r=0.39–0.58, P＜0.05). In the standard length group of 161–183 mm, G. aureolineatus exhibited the highest values of TA (total area) and SEA (standard ellipse area) (6.51 and 1.98, respectively). C. auriga in the 121–140 mm standard length group showed the maximum standard ellipse area corrected (SEAc) value (2.87). For Z. cornutus, the 85–100 mm standard length group had the lowest values of TA, SEA, and SEAc (0.40, 0.38, and 0.51, respectively). Except for N. lituratus and Z. cornutus, the trophic levels of the remaining four fish species increased with increasing standard length groups. Different standard length groups of E. merra exhibited the highest degree of isotopic niche overlap, suggesting intense intraspecific food competition within the species. The isotopic niches among different standard length groups of other fish species exhibited minimal overlap, suggesting that intraspecific food competition was relatively low. This study provides with quantitative evidence for trophic structuring in coral reef fish assemblages around the Qilianyu Islands. The findings will contribute to understanding food web dynamics in the South China Sea coral ecosystems and have implications for marine conservation planning.