The growth of mangroves is inhibited due to environmental degradation, and changes in the growing health of mangrove forests cause changes in internal physicochemical parameters. The canopy chlorophyll content is an important indicator to monitor the health status of mangroves. We study the effective inversion data sources and methods of mangrove health indicator parameters to monitor the health of mangrove ecosystems in typical areas of Beibu Gulf, Guangxi. In this study, we evaluated the capability of UAV, GF-6 data, and machine learning regression algorithms in estimating mangrove species-scale canopy chlorophyll content (CCC). Effective measures for mangrove pest and disease pressure, Sporobolus alterniflorus invasion, and anthropogenic risk are also explored, which are important for mangrove conservation and restoration. (1) We obtained several feature variables by constructing a combined vegetation index, and the most sensitive band of mangrove CCC was selected by the characteristic variable evaluation, and the CCC model at the mangrove species-scale was evaluated and validated. Through variable preferences, the feature variables with the highest contribution of Avicennia marina, Aegiceras corniculatum, Kandelia candel, and a collection of three categories of species in the UAV data were indices of RI35, MDATT413, RI35, and NDI35. (2) Random Forest, Gradient Boosting Regression Tree, and Extreme Gradient Boosting were evaluated using the root-mean-square error and coefficient of determination accuracy metrics. Extreme Gradient Boosting regression algorithms were evaluated for accuracy. In both UAV data and GF-6, RF achieved optimal results in inverse mangrove Aegiceras corniculatum species CCC, with higher stability and robustness in machine learning regressors. (3) Due to the sparse distribution of Kandelia candel in the study area and the low spatial resolution of the images, there is an increased possibility that individual image elements contain environmental noise, such as soil. Therefore, the level of CCC can effectively reflect the health status of mangroves and further reflect the increased possibility of the study area being exposed to risks, such as degradation. The establishment of the current protected areas and restoration of degraded ecosystems are effective measures to cope with the risks of mangrove pest and disease stress, invasion of Sporobolus alterniflorus, and anthropogenic activities, which are important for the protection and restoration of mangroves. This study provides an important data reference and risk warning for mangrove restoration and conservation.