The longjaw tapertail anchovy Coilia nasus, which migrates from ocean to freshwater for spawning in spring, is an important anadromous fish with ecological and cultural significance. To determine parasite infection in anadromous C. nasus, a total of 103 fish from the Yangtze River were collected and examined in 2021 and 2022. The overall infection prevalence of nematodes in C. nasus was 100%, with a mean intensity of 13.81 ± 16.45. The mean intensity of nematode infections in 2022 was significantly higher than that observed in 2021 across all sampling sites (p < 0.05). Nematodes were widely detected in the mesentery, pyloric cecum, stomach, and liver, among which the mesentery accounted for the highest proportion, reaching up to 53.52%. A total of eight ascaridoid nematodes belonging to the family Anisakidae and Raphidascarididae were identified by using morphological characters and molecular biological techniques, including two species of Anisakis, five species of Hysterothylacium, and one species of Raphidascaris. A. pegreffii was found as the predominant species, accounting for 48.65% of all identified parasitic nematodes in liver, while Raphidascaris sp. was the most common nematode in the mesentery, pyloric cecum, and stomach, reaching up to 39.81%, 36.21%, and 74.36%, respectively. The present study systematically investigated the parasitic status and community structure of the nematode in C. nasus during its migration in the Yangtze River. This research provides a foundation for studying the impact of nematode parasitism on the reproductive migration and population recruitment of C. nasus, and offers valuable insights for biomarker screening and nematode identification in C. nasus.