Abstract: With the decline of global eel resources, understanding the spatial distribution patterns of eels, especially the habitat selection of the glass eels, is crucial for elucidating their population behavior mechanisms, identifying migration trajectories, and protecting “hotspots” and “key” areas. Therefore, this study analyzed the characteristics of glass eel resources in the Pearl River estuary based on six stations investigation. This study found that the glass eel resources in the important river estuary along the coast of Guangdong Province gradually decreased from east to west (from Chouzhou to Zhuhai), and the key fishing areas were Lianyang, Rongjiang, and Longjiang River estuaries. Seasonal occurrence from December to March, with a peak in February. Most of the glass eels with a total length about 50 mm, in the form of transparent. The relationship between the spatial distribution of glass eel and environmental factors was analyzed using the Redundancy Analysis (RDA) method, and it was found that the abundance of glass eel showed a spatial autocorrelation relationship. Overall, it was positively affected by runoff and tidal range, negatively affected by water salinity, and greatly influenced by physical environmental factors (such as river runoff, tides, etc.) rather than chemical environmental factors (such as COD, DO, pH, etc.) (P<0.05). As part of long-term investigation of eel resources in the Pearl River system, the results of this study provide basic data for glass eel management in the important river estuary along the coast of Guangdong Province, and are of great significance for clarifying their migration characteristics.