The protection of mangroves through nature reserves has been demonstrated to be effective. There were many studies evaluating the mangrove protection effect. However, the evaluation of mangrove growth quality with positive or negative growth trends, as well as restoration potential against disturbance in nature reserves, is still lacking. Thus, this study proposed a hierarchical evaluation framework for mangrove protection in nature reserves, which takes long-term metrics at three levels of loss and gain areas, patch pattern dynamics, and pixel growth trends into account. The continuous change detection and classification (CCDC) was utilized to identify the change condition of mangroves in six nature reserves of the Guangdong–Hong Kong–Macao Greater Bay Area. The Entropy Weight Technique for Order Preference by Similarity to Ideal Solution (TOPSIS) was utilized for scores evaluation of protection effort comparison from 2000 to 2020. The study results had the following three main findings. Firstly, the mangrove forest area increased by about 294.66 ha in four reserves and slightly decreased by about 58.86 ha in two. Most reserves showed an improved patches intact pattern and more positive growth trends. Secondly, the establishment of nature reserves and afforestation were the main causes of mangrove area gain. Until 2010, aquaculture, agriculture, and urban development were the biggest threats to mangroves. Finally, the protection of the reserves was successful in the early decades, but the general evaluation scores showed a decline in recent years once we considered the growth trends for quality. The proposed hierarchical evaluation methods provide a new sight to research the impacts of abrupt change and protection resilience status of the gradual restoration of nature reserves.