Poyang Lake is the largest freshwater lake in China Extreme flooding and drought occurred in 1998 and 2011, respectively, resulting in a massive loss of aquatic plants. To compare the effects of flooding and drought on aquatic plants and the subsequent recovery process, field investigations were conducted in Poyang Lake National Nature Reserve (PLN) in 2012 and 2014. Historical data from 1984, 1999, and 2001 were also used for comparison. The results revealed that the species composition of aquatic plants after extreme flooding differed from that after extreme drought. After flooding, the species composition was basically the same as the historical records from 1984 under normal hydrological conditions; however, after drought, Najas marina and N. minor disappeared. Moreover, the resilience ability of aquatic plants was higher after extreme flooding than following extreme drought. The dominant species also differed after the two hydrological events. Vallisneria spp. and Hydrilla verticillata were first to recover after flooding, while Vallisneria spp. and Nymphoides peltata recovered fastest after drought. Since extreme drought is more damaging to aquatic vegetation than extreme flooding, we suggest that lakes in the Yangtze River basin aim to maintain a minimum water level through rational regulation of water resources.