Waterlogging, or excessive accumulation of water in the soil, poses significant stress to riparian ecosystems and agroforestry, especially with increasing global rainfall. Cenchrus fungigraminus is a vital agricultural resource, biomaterial, and super-energy plant with high resistance and adaptability. This study examined its morphological and physiological responses under root and above-ground waterlogging for up to 30 days. Results showed that waterlogging significantly inhibited growth, reducing membrane permeability, and root activity, and accelerating leaf senescence (P < 0.05). Despite this, C. fungigraminus achieved 100 % survival after 30 days of waterlogging. The plant adapted to the hypoxic environment by enhancing oxygen channels through cortex cell loosening, lysigenous tissue formation, and adventitious root development. It also activated defense mechanisms, increasing the activities of antioxidant enzymes (SOD, POD, and CAT), levels of non-enzymatic antioxidants (AsA and GSH), osmotic regulators (SS, SP, and Pro), and anaerobic respiratory enzymes (PDC, ADH, and LDH), and hormones (ABA, IAA, GA, and ETH). Under two levels of waterlogging depth, the plant initially adopted the LowO2 escape strategy (LOES), but over time, it transitioned to the Low-O2 quiescence strategy (LOQS), while still retaining some features of the LOES. Our results revealed that C. fungigraminus demonstrates strong adaptability to waterlogging, especially in response to root waterlogging. By employing anatomical adjustments and exceptional cellular defense mechanisms, the species effectively mitigates damage, establishing itself as an excellent forage grass for slope protection under waterlogged conditions. These results offer valuable guidance for selecting waterlogging-tolerant species to restore and rehabilitate degraded riparian ecosystems in the Yellow River Basin, optimize land use in waterlogging-prone areas, and advance the genetic improvement of waterlogging tolerance in other forage varieties.