Poyang Lake is a typical lake that links to rivers in the middle and lower reaches of the Changjiang River. The outflow characteristics and water level fluctuation of Poyang Lake are affected by the flow from Ganjiang River, Fuhe River, Xinjiang River, Raohe River, Xiushui River and the Changjiang River, forming a complex hydrological relationship between rivers and lakes. According to hydrological data of the aforementioned five rivers and the control hydrological station of Poyang Lake from 1956 to 2016, we probed into the variations of water recharge from the Changjiang River into Poyang Lake via wavelet analysis and other methods. Research results revealed that the average annual runoff from 2003 to 2016 was lower than that from 1956 to 2002. The volume and number of days of water recharge are both positively correlated with the difference between the streamflow of Hankou Station and the amount of runoff entering Poyang Lake. After 2003, the impounding or releasing of the Three Gorges Reservoir has, to some extent, affected the seasonal changes of the rivers and lakes and the drought and flood opportunities in the Poyang Lake Basin, and further reduced the frequency of water recharge from the Changjiang River into Poyang Lake. In the 1960s, 1980s and early 21st century, the incoming flow from the upper and middle reaches of the Changjiang River exerted strong influence on Poyang Lake; and in the 1970s, 1990s and 2010s, such influence weakened. The research findings are of great significance for understanding the relationship between the Changjiang River and the Poyang Lake under varying circumstances.