River-connected lakes in the midstream and downstream of Changjiang River have functions of flood storage and water resources conservation. With the Three Gorges Project as node, current research on river-connected lakes in the midstream and downstream of Changjiang River is in lack of supportive analysis. Research on the annual evolution of backward flow in river-connected lakes under changing environment is insufficient as well. In view of this, the backward flow measured at Hukou Station, Poyang Lake was divided into the series before alteration point and the series after alteration point to study the inner-annual allocation of backward flow. Hydrological Alteration Diagnose System was adopted to analyze the water level series of Hukou Station to uncover the alteration point. Results show that despite increased monthly mean backward flow rate after alteration point, the duration and backflow flow volume both decreased, and the extreme value of backward flow declined dramatically, which was conducive to the safety of flood control of Poyang Lake. The monthly mean backward flow rate, duration, and extreme value of backward flow rate in non-flood season were greatly smaller than those before the alteration point, posing large impact on the water level of Poyang Lake in dry season. The results offer reference for analyzing the water regime of river-connected lakes in changing environment.