Watershed hydrological cycle has been changed along with the intensifying frequency of extreme water events due to the influence of climate change and human activities. Poyang Lake, the largest freshwater lake in China, is a lake naturally connected with the Changjiang River. The complicated river-lake interactions impact the hydrological rhythm of lake, which will further influence water security associated with flood control, drinking water usage, water pollution and water ecology in the lake basin. In the case, it is of great importance for maintaining watershed water security to understand the characteristics of hydrological rhythm variation in terms of river-lake interactions. In this study, temporal variation of hydrological rhythm in Poyang Lake and the associated water exchange with the Changjiang River were analyzed based on the measured hydrological data of 4 gauge stations in Poyang Lake area along with other data from the Hukou station at the intersection between the Changjiang River and Poyang Lake in 1951-2011. The major findings are shown as follows: the span of dry season increased since water level remains low in November and April. Meanwhile, the span of flood season decreased in 2000s. The lower water level in rising season and retreating season make Poyang Lake rising later but falling earlier than they did in 1980-2002, thus shortening the conversion time of the lake from flood situation to dry situation. Further, the peak flow in the annual hydrograph has been shifted. The primary cause of hydrological rhythm variation is the water exchange between the main stream of the Changjiang River and Poyang Lake. In 2000s, changes in the water level of the Changjiang River altered the interaction between the river and Poyang Lake through the slope of water surface, disturbing the lake basin hydrological processes and resulted in disordering of hydrological rhythm in Poyang Lake. The increasing discharge from the lake to the river in retreating season lead to the lake enter dry season earlier. And the declining water level of Changjiang River in rising season lead to the addition of lake water continued to leak river, thus the lake rose slowly. For the reasons given above, the variation of water supplement of Poyang Lake on the Changjiang River mainstream in 2000s altered the hydrological rhythm in Poyang Lake. Results of this study improve our understanding of Poyang Lake hydrological rhythm consequences of river-lake relationship changes, and it provides knowledge for long-term planning for effectively restoring nature's innate rhythms for sustainability and productivity in the Poyang Lake Basin. In addition, the results will help further explore the coordinate and healthy river-lake relationships.