To comprehensively assess the ecological status of the wetlands in the Anhui Chinese Alligator National Nature Reserve, this study conducted investigations on water quality, wetland animal and plant resources, invasive species resources, etc., in this area. Countermeasures for the areas that need improvement in the monitoring work were proposed. The results showed that the water quality at monitoring points 3, 4, 5 and 6 was relatively poor, with indicators such as ammonia nitrogen and total nitrogen partly exceeding the standard; the wetland plant habitats in the study area were diverse, with 4 vegetation type groups, 10 vegetation types and 85 clusters. The bird species were relatively rich, with a total of 13 orders, 27 families and 53 species. Among them, Passeriformes had the largest number of birds, while non-Passeriformes have the largest numbers of Pelicans and Charadrians. Amphibians consisted of 2 orders, 6 families and 8 species, including Hoplobatrachus chinensis, Fejervarya multistriata, Pelophylax nigromaculatus, etc. There were 3 orders, 7 families and 9 species of reptiles, including Gloydius brevicaudus, Sinonatrix annularis, Zaocys dhumnades, etc. Benthic animal biodiversity was relatively high and evenly distributed, with 3 phyla, 5 classes, 20 families and 38 species (genera). There were 24 species of invasive alien plants from 13 families, including Phytolacca americana, Dysphania ambrosioides, Amaranthus hybridus, most of which belong to the Compositae family. There are areas in wetland protection work that need further improvement, such as water environment, scientific research and monitoring levels, and public publicity. Based on this, suggestions such as strengthening ecological protection and restoration, improving scientific monitoring, and enhancing publicity work are put forward to effectively protect the biodiversity in the research area. This article provides a reference for the scientific protection and breeding of Chinese alligators.