Stand structural configuration dictates ecosystem functional performance. Mangrove ecosystems, located in ecologically sensitive coastal ecotones, require efficient acquisition of stand structure parameters and health assessments based on these parameters for practical applications. Effective assessment of mangrove ecosystem health, crucial for their functional performance in ecologically sensitive coastal ecotones, relies on efficient acquisition of stand structure parameters. This study developed a UAV (Unmanned Aerial Vehicle)-based framework for mangrove health evaluation integrating stand structure parameters, utilizing UAV visible-light imagery, field plot surveys, and computer vision techniques, and applied it to the assessment of a national nature reserve. We obtained the following results: (1) A deep neural network, combining UAV visible-light data with tree height constraints, achieved 88.29% overall accuracy in simultaneously identifying six dominant mangrove species; (2) Stand structure parameters were derived based on individual tree extraction results in seedling zones along forest edges (with canopy individual tree segmentation accuracy ≥ 78.57%), and a stand health evaluation model was constructed; (3) Health assessment revealed that the core zone exhibited significantly superior stand health compared to non-core zones. This method demonstrates high efficiency, significantly reducing the time and effort for monitoring, and offers robust support for future mangrove forest health assessments and adaptive conservation strategies.