[Objectives] The National Nature Reserve of Guangdong Nanpeng Islands is the only national marine ecological reserve in the eastern Guangdong region, characterized by a rich diversity of marine species, including crabs (Decapoda:Brachyura). However, the status of these crab populations remains largely unknown, hindering effective scientific research and conservation efforts for these species. Therefore, this study aims to conduct a field survey encompassing both the coral reef ecosystem and the shallow continental shelf ecosystem (herein referred to as non-coral reef habitats) to investigate species diversity, community structure, and to update the regional species list of crabs within the National Nature Reserve of Guangdong Nanpeng Islands. [Methods] Field surveys were conducted using trawl and diving methods in June 2023 and June 2024 to assess crab species across 25 sites within the National Nature Reserve of Guangdong Nanpeng Islands (Fig. 1). Of these sites, 10 were located in non-reef areas, while 15 were situated in coral reef regions, representing the majority of crab habitats in this region. We analyzed the structure of the crab community using Pianka’s Index of Relative Importance (IRI), the Hill diversity index, and the Jaccard similarity index. To estimate potential species diversity, we employed statistical extrapolation and interpolation methods. To identify the key species contributing to variations in community composition, we performed SIMPER analysis. Additionally, we conducted non-metric multidimensional saling (NMDS) analysis to explore the spatial distribution patterns of crabs, and utilized one-way analysis of variance (ANOVA) to assess the significance of differences in community structure. [Results] A total of 36 crab species belonging to 12 families and 22 genera were documented in this survey. Species richness was greater in the coral reef area, which harbored 27 species, compared to the non-reef area, which contained 23 species. At the family level, the highest abundance was observed in the Portunidae and Calappidae families, while at the genus level, the Portunus and Calappa genera exhibited the greatest abundance (Fig. 2a). The Portunidae and Xanthidae families demonstrated the highest species diversity, whereas the Charybdis and Portunus genera were the richest at the genus level (Fig. 2b). To evaluate the potential species diversity of the two regions, we assessed sample coverage and conducted statistical extrapolation. The coral reef area exhibited a sample coverage of 87.50%, whereas the non-reef area achieved a coverage of 99.99% (Fig. 3a). Statistical extrapolation indicated that the coral reef could potentially support up to 83 species, which is significantly higher than the estimated 26 species for the non-reef area (Fig. 3b). The non-metric multidimensional scaling (NMDS) analysis revealed significant differences in crab community structure between the coral reef and non-reef areas (ANOSIM:R = 0.540 8, P = 0.001; Jaccard similarity index:0.361) (Fig. 4). The low similarity between the two habitats may be attributed to differences in species composition and the presence of numerous habitat-specific species. For example, the dominant species in the coral reef area was Charybdis acuta, while Portunus sanguinolentus was the dominant species in the non-reef area. In addition, species from the family Euryplacidae were exclusively found in the non-reef area, whereas species from the families Inachidae, Tetraliidae, and Percnidae were exclusively distributed in the coral reef area. By integrating historical records with our survey data, the regional crab species list has been updated to encompass 99 species from 26 families and 66 genera, including 15 newly recorded species. [Conclusion] This study highlights the significance of conducting comprehensive surveys of crab fauna across various habitats, particularly coral reefs. It also provides critical data for the scientific management and conservation of crab resources within the National Nature Reserve of the Guangdong Nanpeng Islands.