Yellowfin sea bream (Acanthopagrus latus), an economically important fish and stock enhancement species, is distributed in the southeastern coastal areas of China. Study on diet change of yellowfin sea bream will contribute to the knowledge for the accurate food composition and ecological function of food wed for yellowfin sea bream. However, information on the feeding habits of wild yellowfin sea bream in natural marine environments is scarce. In this study, the feeding characteristics of yellowfin sea bream of different body lengths (1-3 years old) collected from the Wanshan Islands were analyzed based on stomach morphology and high-throughput sequencing of the 18S rRNA. Here, the 17 collected fishes were divided into three groups: the S group [body length: (194±13.1) mm], the M group [body length: (231±15.5) mm], and the L group [body length: (294±33.3) mm]. Morphological identification showed that shellfish, crabs, and chyme were present in the stomach contents of the yellowfin sea bream. Most fish contained a high proportion of chyme. A total of 84 species of eukaryotes in 16 phyla were identified in the stomach contents of the yellowfin sea bream using high-throughput sequencing of the 18S rRNA gene. Therefore, 18S rRNA high-throughput sequencing analysis provided a higher taxonomic resolution of the dietary composition than microscopic examination. Furthermore, high-throughput sequencing analyses showed that the major food sources of yellowfin sea bream were Charybdis feriatus and Centropages abdominalis of Arthropoda, Brachidontes variabilis of Mollusca, Nematalosa nasus of Chordata, and Neopyropia yezoensis of Rhodophyta, accounting for 66.73% of total food sources. Yellowfin sea bream in the Wanshan Islands mainly fed on animal food and feeding on plant food was relatively low. At the phylum level, the S group were dominant with Arthropoda, Mollusca and Rhodophyta, accounting for 93.88% of all sequences. Chordata, Cnidaria, and Arthropoda were the dominant phyla in the M group, accounting for 86.72% of all sequences, whereas L group was dominated by Chordata, Platyhelminthes, and Arthropoda, accounting for 89.25% of all sequences. Diet analysis of 1-3-year-old yellowfin sea bream revealed that with an increase in body length, the major feeding species of yellowfin sea bream gradually shifted from Arthropoda and Mollusca to Chordata, and the number of feeding species gradually decreased. Compared with that of the other Sparidae fishes in the Pearl River Estuary, a similar dietary habit was observed between Sparidae fishes, indicating feed-food competition for Sparidae fishes from the Pearl River Estuary. Sparidae are omnivorous and mostly consume benthos, plankton, and fish. These results provide basic data on the feeding ecology of yellowfin sea bream in the Wanshan Islands.