To analyze daily variations in Anguilla japonica glass eel catch as related to ecological factors at Jingjiang section of the Yangtze River, we conducted daily monitoring program at Jingjiang section of the Yangtze River during the 2012 fishing season. A generalized additive model (GAM) was applied to evaluate the relationships between daily catch and their ecological variables, including water temperature, the tidal range, turbidity, lunar phase, tide phase and pressure. Fishing was performed at Jingjiang section of the Yangtze River from late January to early April. The total fishing period catch per boat ranged from 221 ind. to 443 ind. with a mean±SD of (344.8±83.4) ind. The daily catch differed by month. The mean daily catch was only 0.4 ind./d in January, and the abortive haul rate was 90.9%; while mean daily catch was up to 10.4 ind./d in April, and the abortive haul rate was only 10.0%. Stepwise GAM building using the AIC and adjusted pseudo-R² showed that turbidity, pressure and lunar phase did not affect daily catch of A. japonica glass eels significantly, but three predictor variables, tide phase-month interaction, water temperature and tidal range were highly significant. In addition, tide phase-month interaction, water temperature, and tidal range account for 42.4%, 19.1% and 13.1% of the variance in the data, respectively, and these three variables also showed a positive relationship with the daily catch. Statistical results also showed that the daily catch fluctuated with tide phase, since high catches appeared at times corresponding to the spring tide of the full moon or the new moon, while, low catches appeared at times corresponding to the neap tide during quarter moons. Moreover, glass eels were caught when the minimum water temperature was 6.3℃, and a greater catch was found in optimal water temperature ranging between 10 and 15℃. Overall, the proportion of total catches for spring or neap tide period was 76.8% and 23.2%, respectively. Furthermore, our results suggested that during glass eels upstream migration using ‘selective tidal stream transport’, some individuals were captured in the mouth zone of the Yangtze estuary, and some individuals preferred to stay near the river section of the estuary, whereas others migrated upstream. In our study, water temperature, tidal range and tide phase were the important ecological factors affecting the fluctuations in upstream migration of glass eels.