As renowned "ecosystem engineers," oyster reefs perform crucial ecological functions such as water purification, providing habitats and shelters for other organisms, and stabilizing coastal lines. As an important component of blue carbon sinks, oyster reefs sequester carbon by absorbing carbon dioxide from seawater and undergoing calcification, biological assimilation, and sedimentation, thereby achieving carbon fixation. However, global wild oyster resources have declined sharply—over the past century, the global area of oyster reefs has decreased by nearly 85%, leading to the destruction or loss of the ecological structure and functions of oyster reef habitats. Currently, most studies on oyster reefs in China focus on temperate regions, with relatively few studies in tropical waters, especially in the coastal waters of Hainan Island. Investigating the community structure and carbon stock of oyster reefs along the coast of Hainan Island will be more conducive to the protection and restoration of coastal ecosystems in China. To fill this knowledge gap, we conducted sampling and environmental monitoring across 12 oyster reef areas along the coast of Hainan Island. Based on preliminary surveys, these reef areas were categorized into four habitat types: estuarine oyster reefs, intertidal natural oyster reefs, mangrove oyster reefs, and coastal engineering area oyster reefs. The research methodology comprised the following steps to ensure comprehensive and accurate data collection. First, aerial imagery captured by drones was used to photograph sampling sites, and specialized software was applied to delineate reef boundaries and areas. These measurements were integrated with satellite imagery to estimate total reef area and oyster coverage. For specific stations requiring validation, on-site surveys were conducted to verify spatial data. Second, a multi-parameter water quality analyzer was used to determine seawater temperature, salinity, pH, and chlorophyll-a concentration, to characterize the aquatic environment of each reef area. Third, depending on habitat type, quadrats of appropriate sizes were established for quantitative sampling, supplemented by qualitative collection in surrounding areas. After rinsing and screening, samples were stored at low temperatures and transported to the laboratory for further analysis. Fourth, all reef-dwelling organisms were identified and quantified using standard taxonomic guides. In detail, oyster samples were identified to the species level via molecular methods, while other reef-dwelling organisms were identified to family level. Species composition, oyster diversity and proportional abundance, as well as the abundance and wet weight of live oysters and other reef-dwelling taxa were recorded for subsequent community analysis. Finally, Dried shells, soft tissues, and shell debris from reef-dwelling shellfish were ground, sieved, and stored separately. Carbon content was measured using an elemental analyzer, and oyster reef carbon storage was quantified applying the standard shellfish carbon sequestration equation. The results of this study are as follows: (1) A total of 53 species of reef-dwelling organisms were identified, belonging to 7 phyla, 9 classes, 18 orders, and 28 families, with Bivalvia and Gastropoda being the dominant classes. (2) A total of eight oyster species were identified. Saccostrea malabonensis was the dominant species at most survey stations (except in Longlou town and Guoheyuan) with relative abundance ranging from 6.25% to 100%. Saccostrea mordax was primarily found in intertidal natural oyster reef areas, accounting for 93.75% and 50% of the relative abundance in Longlou town and Huiwen town, respectively. Crassostrea iredalei was distributed across all surveyed habitats except for intertidal natural oyster reefs. (3) Among the four habitats, the species diversity index (H′) and richness index (d) of intertidal natural oyster reefs were higher than those of other habitats, with the highest values recorded at Haitou town (1.83 for H′ and 3.28 for d), followed by estuarine oyster reefs and mangrove oyster reefs, while coastal engineering area oyster reefs had the lowest indices, indicating that intertidal natural oyster reefs provide a more favorable habitat for reef-dwelling organisms. (4) The composition of reef-dwelling organisms and the content of shell remains varied significantly among stations: intertidal oyster reefs were mainly composed of live oysters (12.8%–77.9%) and shell remains (8.7%–86.7%); estuarine oyster reefs and coastal engineering area oyster reefs contained higher proportions of shell remains (67.2%–79.6%); and mangrove oyster reefs had higher biomass of other reef-dwelling shellfish (e.g., mussels and beach snails, 12.4%–28.9%). (5) In terms of biomass and carbon stock of reef-dwelling organisms in different oyster reef habitats, intertidal natural oyster reefs had significantly higher total biomass and total carbon stock than other habitats, with Haitou town showing the highest value (total live biomass: 49,760.86 t; shell remains: 46,503.71 t; total carbon stock: 14,844.48 t C). Through field surveys and measurements of carbon content in shell and soft tissues of reef-dwelling shellfish, this study systematically investigated the species composition, community structure, and their relationships with environmental factors across different oyster reef habitats. It also quantified the biomass and carbon storage of reef-dwelling shellfish in these habitats. The results provide valuable data to support the protection and restoration of oyster reef ecosystems, particularly in understudied tropical coastal regions such as Hainan Island. This research enhances the understanding of coastal ecosystem dynamics and strengthens the scientific basis for ecological conservation and restoration efforts in China's coastal zones.