Flooding is one of the most common abiotic stresses that plants suffer. Roots are organs that directly sense anoxic environments, but there are few researches on the response of roots to flooding. In this research, the responses of male and female Salix viminalis plants to flooding were investigated by examining the morphological and physiological responses of roots. Our results showed that primary roots (PRs) growth was significantly inhibited and damaged to a certain extent. However, adventitious roots (ARs) formed in a short time and were essential for plants to endure flooding. To cope with flooding stress, the antioxidant enzyme activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), ascorbate peroxidase (APX) increased. Although Pro-contents increased, they were too low to contribute significantly to osmotic adjustment. The anaerobic respiration metabolic pathway was also activated, as proven by increased pyruvate decarboxylase (PDC), alcohol dehydrogenase (ADH), and lactate dehydrogenase (LDH) activities, and the ethanol metabolism pathway might have a key function in adapting to the hypoxic environment for S. viminalis. In addition, increased non-structural carbohydrates (NSCs) of starch and soluble sugar (SS) contents indicated that quiescence strategy might exist in S. viminalis. Overall, there were no significant differences between males and females under flooding stress, and both genders exhibited strong adaptability to the flooding environment. Therefore, two genders of S. viminalis could be applied in the riparian zone.