By studying the structural characteristics and carbon storage of the mangrove island ecosystem in the Beibu Gulf, this study provides a scientific basis for mangrove ecological compensation in the coastal areas of Guangxi, South China Sea. On the basis of the unmanned aerial vehicle remote sensing images and a sample plot survey, the object-oriented multi-scale segmentation algorithm is used to extract the mangrove community type information, and one-way analysis of variance is conducted to analyse the structural characteristics of the mangrove community. The carbon storage and carbon density of different mangrove ecosystems were obtained based on the allometric growth equation of mangrove plants. The analysis yielded four main results. (1) The island group covers about 27.10 ha, 41.32% (11.20 ha) of which represents mangrove areas. The mangrove forest is widely distributed in the tidal flats around the islands. (2) The main mangrove types were Aegiceras corniculatum, Kandelia obovata + Aegiceras corniculatum, Avicennia marina + Aegiceras corniculatum and Avicennia marina communities. (3) Amongst the mangrove plants, Avicennia marina had the highest biomass (18.52 kg plant^–1), followed by Kandelia obovata (7.84 kg plant^–1) and Aegiceras corniculatum (3.85 kg plant^–1). (4) The mangrove carbon density difference was significant. Kandelia obovata had the highest carbon density (148.03 t ha^–1), followed by Avicennia marina (104.79 t ha^–1) and Aegiceras corniculatum (99.24 t ha^–1). The carbon storage of the mangrove island ecosystem was 1194.70 t, which was higher than in other areas with the same latitude. The carbon sequestration capacity of the mangrove was relatively strong.