Climate change affects the distribution of fish species and thus alters the pattern of fish abundance. However, effects of climate change on China coastal fisheries have not been studied yet. Estuaries play an important role in the function of marine ecosystem, hence they are key habitats for many fishery species and form ideal fishing grounds. Here we investigated the impacts of climate change on fish abundance by estimating the distribution of dominant and important species in the Yangtze River estuary. The analysis was performed using the dynamic bioclimate envelope mode, and the distribution data of fishery species were based on the survey during 2012-2013 in the Yangtze River estuary. Three climate change scenarios (RCP2.6, RCP6.0 and RCP8.5) were evaluated combined with the projection data from the Geophysical Fluid Dynamics Laboratory. The water temperature in the Yangtze River estuary was estimated. Without human activities, the increment of fish abundance, particularly the demersal fish abundance, increased over time in all three climate change scenarios. The increment and the distribution followed the order RCP8.5>RCP6.0>RCP2.6. The distribution of fish abundance increment in RCP8.5 was wider than those in the other two scenarios. It is expected that the fish abundance increment will be mainly in the north of the Yangtze River estuary in 2020 and 2030, and in 2050 the increment may migrate to the southern part, and there will be less increment in the offshore water body of the Yangtze River estuary. The center of fish abundance increment will be mainly located in the coastal area of the Chongming Island. These results suggest that the climate change greatly contributes to the fish abundance distribution in the Yangtze River estuary, and that the effects of climate change on fish abundance distribution vary in different scenarios. Therefore, climate change should be considered in the future adaptive fishery management in the coastal waters.