<p>The South China Sea (SCS), due to its unique geographical location and marine environment, harbors a diverse and representative coral reef ecosystem. This study examines the trophic structure of major marine organisms within the coral reef ecosystem of the southern SCS through stable isotope analysis (δ¹³C and δ¹⁵N). The analysis is based on field samples collected during the spring of 2023 and 2024. The δ¹³C values of consumers spanned from −21.72‰ to −3.26‰, and the δ¹⁵N values ranged from 2.42‰ to 10.97‰, which indicates a well-defined and continuous trophic spectrum. The trophic levels (TLs) of fish varied from 1.80 to 3.35, whereas those of invertebrates ranged from 1.08 to 2.76, suggesting a structured ecosystem in the study area. MixSIAR modeling revealed that macroalgae, plankton, and organic matter on coral surfaces (OMCs) were the predominant basal food sources, supporting five major trophic groups: carnivores, corallivores, planktivores, macroalgae-consuming herbivores and omnivores. Notably, several species that traditionally feed on coral, such as <i>Chaetodon ornatissimus</i> and <i>Heniochus chrysostomus</i>, demonstrated an increased reliance on algal resources, implying a possible change in feeding strategy. Additionally, the diet preference of <i>Acanthaster planci</i> showed a strong reliance on crustose coralline algae (CCA), with juveniles experiencing growth stagnation or adults suffering from long-term starvation being the predominant individuals. This highlights the importance of food-source monitoring for understanding the population dynamics of <i>A. planci</i>. This study provides basic data and novel perspectives for coral reef conservation and sustainable management in the coral reef ecosystems of the western Pacific Ocean.</p>