[Aim] To investigate species diversity and community patterns of freshwater fish and assess the potential invasiveness of non-native fish in the Beijing area.[Method] We sampled 33 sites from three types of freshwater ecosystems in Beijing, including reservoirs, lakes, and rivers, during June 10-17, 2020. We used the environmental DNA metabarcoding approach to analyze species diversity, classified the identified fish into native and non-native species. Lastly, a risk-screening procedure was performed to assess the invasion risk of alien invasive fish in Beijing using the Aquatic Species Invasiveness Screening Kit (AS-ISK).[Result] We detected 52 species of freshwater fishes belonging to seven orders, 22 families, and 43 genera. First, based on the PCOA and ANOSIM analyses, we found no significant difference in fish diversity and community composition in reservoirs, lakes, and rivers. Most of the dominant species were shared among three water types, and few were unique. Both the fish diversity and biomass at sites sampled from mountainous regions were higher than those from the urban regions, suggesting that human activities and urbanization could significantly influence freshwater fish diversity and community composition. Species richness of fish in Beijing was lower compared to historical records. A total of 39 native fish were detected in our study, which was far lower than the previous record of 83 species. We detected an increasing number of alien fish, including six invasive species, namely, Ov niloticus, Micropterus salmoides, Clarias batrachus, Clarias gabonensis, Chitala ornate, and Oreochromis tanganicae. Finally, the invasion risk assessment revealed that all six invasive fish showed high invasion risk in Beijing, which could seriously affect local species diversity, indicating that we should pay increasing attention to their population dynamics.[Conclusion] In this study, we adopted the environmental DNA metabarcoding technology to assess species diversity of freshwater fishes in Beijing. Our findings not only contribute to a better understanding of the background data of fish resources in Beijing at present, but also provide appropriate guidance for the protection of native fishes and management of alien invasive fish.