Seagrass coverage ratio is an important indicator reflecting the ecological status of seagrass beds. In this paper, through the design of aerial photography scheme and flight condition test, the high-resolution seagrass image map of the Dongjiao Coconut Forest sea area was obtained by using UAV aerial photography. Combined with the image classification tools of ArcGIS software and 3D tools, a new method for calculating the coverage ratio of seagrass were obtained and the coverage of seagrass was calculated. The station location of simulating survey method of the traditional seagrass coverage ratio was compared and discussed. Seagrasses in the coastal sea bed of the Dongjiao Coconut Forest are distributed on the coral reefs within 300 m from the shore with patches and intervals. Using the new method, the concentrated distribution area of seagrass at sea bed of the Dongjiao Coconut Forest is about 23 221 m², and average concentration distribution ratio is 17.79%. The distribution area of seagrass in this study area is about 16 423 m², and the coverage ratio of seagrass is 12.58%. The coverage ratio of seagrass is higher, and the ecological condition of seagrass bed is good. Sargassum is densely distributed in the southeast area of the study area, with a distribution area of 755.6 m² and a coverage of 0.5%, and grows as a single cylinder floating. By simulating the investigation station location of the sample frame method and sample line method of traditional seagrass coverage survey, seagrass coverage ratio changes with different stations, sample frame, and sample line positions changing randomly, which is the reason for the representativeness and comparability of the traditional survey results. The research results of this project have the promotion and application value in the investigation of seagrass ecological monitoring area.