Mapping the distribution of living and dead trees in forests, particularly in ecologically fragile areas where forests serve as crucial ecological environments, is essential for assessing forest health, carbon storage capacity, and biodiversity. Convolutional neural networks, including Mask R-CNN, can assist in rapid and accurate forest monitoring. In this study, Mask R-CNN was employed to detect the crowns of Casuarina equisetifolia and to distinguish between live and dead trees in the Pingtan Comprehensive Pilot Zone, Fujian, China. High-resolution images of five plots were obtained using a multispectral Unmanned Aerial Vehicle. Six band combinations and derivatives, RGB, RGB-digital surface model (DSM), Multispectral, Multispectral-DSM, Vegetation Index, and Vegetation-Index-DSM, were used for tree crown detection and classification of live and dead trees. Five-fold cross-validation was employed to divide the manually annotated dataset of 21,800 live trees and 7157 dead trees into training and validation sets, which were used for training and validating the Mask R-CNN models. The results demonstrate that the RGB band combination achieved the most effective detection performance for live trees (average F1 score = 74.75%, IoU = 70.85%). The RGB–DSM combination exhibited the highest accuracy for dead trees (average F1 score = 71.16%, IoU = 68.28%). The detection performance for dead trees was lower than for live trees, which may be due to the similar spectral features across the images and the similarity of dead trees to the background, resulting in false identification. For the simultaneous detection of living and dead trees, the RGB combination produced the most promising results (average F1 score = 74.18%, IoU = 69.8%). It demonstrates that the Mask R-CNN model can achieve promising results for the detection of live and dead trees. Our study could provide forest managers with detailed information on the forest condition, which has the potential to improve forest management.