The fishway of the Xiajiang Hydro-Junction was built to meet the needs of breeding and over-wintering migratory fish. To alleviate the effects of its operation, netting and interception methods were used to conduct surveys to determine the effects of the fish passage at the Xiajiang Hydro-Junction during October 2019, January 2020, April 2020, and August 2020. A total of 4605 fishes was collected, including 42 species belonging to 4 orders, 9 families, and 34 genera, mainly small- and medium-sized fishes. The body length ranged from 2.3 cm to 48.5 cm. The dominant species were Zacco platypus, Squalidus argentatus, Saurogobio dabryi, Culter alburnus, and Pelteobagrus fulvidraco, accounting for 17.24%, 14.26%, 6.86%, 5.78%, and 4.89%, respectively. The migratory fishes in the fishway included Ctenopharyngodon idella, Squaliobarbus curriculus, Pseudobrama simoni, and Anguilla japonica. The number of passing fish varied seasonally and was the highest during summer, accounting for 42.23% of the total, whereas the number was the lowest during winter, accounting for 11.69% of the total. Factors affecting fish passing were mainly water temperature and water level. There were 42 species of fish passing through the entrance of the fishway of the Xiajiang Hydro-Junction. There were more species of fishes passing through the fishway of the Xiajiang Hydro-Junction than those through other fishways. These results will provide reference data for the optimization and effective operation of fishways, which could have implications in the protection of fishery resources in the Ganjiang River.