This study aimed to investigate the adaptive mechanisms of mulberry (Morus alba) to waterlogged conditions, with a specific focus on the development of adventitious roots (ARs), alteration of growth strategies, and adjustment of chlorophyll fluorescence parameters. To achieve this goal, 4-year-old potted mulberry plants were selected for research, and a waterlogging simulation method was implemented. Four treatments were established to investigate the effects of varying water conditions on leaf waterlogging damage, the number of ARs, plant height, chlorophyll fluorescence parameters, and proton motive force (pmf) parameters in mulberry plants. These treatments included the control group (CK), shallow submerged group (SS), half-submerged group (HS) and deep submerged group (DS). Our results showed that (1) The number of ARs in each group increased with increasing waterlogging time. (2) Waterlogging stress inhibited the height growth of mulberry, and the changes in plant height in the HS and DS groups were significantly lower than those in the CK and SS groups. (3) The maximum photochemical quantum yield (Fv/Fm) in the HS and DS groups decreased significantly under waterlogging stress. The nonphotochemical quenching (NPQt) of mulberry leaves in the submergence group increased significantly in the early stage of waterlogging stress, and the NPQt in the submergence group increased continuously with increasing waterlogging time. (4) Thylakoid conductivity to protons (gH+) in the leaves of mulberry decreased significantly under waterlogging stress, whereas the steady-state rate of proton flux (vH+) and total electrochromic shift (ECSt) increased significantly. The morphological, physiological, and ecological responses of mulberry plants to waterlogging stress include the timely generation of ARs at the stem base, the adjustment of plant growth strategies, and the repair of photosynthetic response centers in leaves through heat dissipation and thylakoid acidification mechanisms.