Lateral hydrological connectivity (LHC) maintains the high biodiversity and ecosystem functions in the river–floodplain system. We investigated the changes in the taxonomic and functional composition of fish assemblages in the lateral connection channel between the Yangtze River and Poyang Lake, China, during the dry and wet seasons and which factors drive the changes. The results indicated more lake‐residence species and fewer river–lake species in the channel during the wet season than the dry season, leading to significant seasonal differences in taxonomic compositions and trait patterns. Water temperature, water level and fish migration influenced fish assemblage structures in the channel. Water‐level fluctuations that limited food sources and suitable habitats promoted the migration of riverine and lake‐residence fish during both seasons. Water temperature and level also significantly influenced species‐specific migration. Water temperature influenced the spawning migration of river–lake fish during the wet season. Based on these results, we found temporal species‐specific migration dynamics in fish assemblages in the lateral channel that were related to species’ life‐history traits. Therefore, we inferred that the temporal–spatial interaction of the fish community in the river–floodplain system is essentially derived from the evolutionary adaption to the monsoon climate. This process is well studied and predictable, and can be beneficial for managing the river–floodplain systems. The invasion risk of the exotic species, including fish and macroinvertebrates, should be assessed before implementing LHC restoration.