[Aim] The aim of this study was to reveal the difference of growth and physiological characteristics between Bidens alba and its native congeneric B. biternata under waterlogging stress.[Method] The changes of plant height, number of new adventitious roots, net photosynthetic rate (P_n), total biomass, relative growth rate, leaf area and other growth and physiological indicators of B. alba and B. biternata were studied under control and waterlogging stress.[Result] B. alba maintained a higher plant height, the number of new adventitious roots, and P_n (P<0.01), total biomass, relative growth rate, root biomass, stem biomass, leaf biomass and leaf area (P<0.05) than the native B. biternata during waterlogging stress. The dehydrogenase activity of roots and maximum quantum yield of photosystem II of B. alba was significantly higher than that of B. biternata (P<0.05) within 10 days of waterlogging stress, but those parameters tended to be consistent after 20 days of waterlogging stress, indicating that the negative effects of waterlogging on invasive B. alba were less than the native B. biternata. The faster growth rate of new adventitious roots and the higher dehydrogenase activity of roots in the early stage of waterlogging stress could alleviate the stress of waterlogging on the invasive B. alba, which would reduce the damage of waterlogging to the photosynthetic system, and maintain a higher P_n, thus contributing to a higher growth rate of B. alba. These results explained the tolerance mechanism of B. alba to waterlogging.[Conclusion] Compared with the native B. biternata, short-term waterlogging can make the invasive B. alba form a growth advantage, and the waterlogging caused by the short-term concentrated precipitation of the rainy season in southern China is conducive to the invasion of B. alba. The imbalance of precipitation caused by global climate change might exacerbate the invasion of B. alba in southern China.