Abstract: The Pearl River Estuary is an important fishing ground and conservation area for aquatic resources in China. In order to understand the current situation and change trend of fishery resources in the Pearl River Estuary, we carried out six bottom trawl surveys in the spring and autumn of 2018–2023, and explored the composition of fish community structure in the Pearl River Estuary waters and its relationship with environmental factors, so as to provide a basis for scientific management and effective protection of fishery resources. The results show that a total of 168 fish species had been identified from the six surveys, belonging to 17 orders, 55 families and 119 genera. The dominant and important species were mainly small and medium-sized bottom-layer fish, including Leiognathus brevirostris, Collichthys lucidus, Osteomugil ophuyseni, Ilisha elongata, Coilia grayi and Odontamblyopus rubicundus. The average stock density and tail stock density of fish showed both seasonal and interannual variations among the six surveys, with the highest values in spring of 2020 and autumn of 2020, respectively. The cluster analysis shows that the fish community of spring surveys was divided into four groups with both interannual and spatial differences. However, the fish community in autumn surveys was divided into three groups with only interannual heterogeneity. Canonical correspondence analysis (CCA) indicates that salinity, water temperature and water depth were the main environmental factors affecting the community structure of fish in spring, while transparency, contents of active phosphate, water depth and water temperature were the important factors influencing fish community structure in autumn.