Purple nutsedge (Cyperus rotundus L.) is one of the world’s resilient upland weeds, primarily spreading through its tubers. Its emergence in rice fields has been increasing, likely due to changing paddy farming practices. This study aimed to investigate how C. rotundus, an upland weed, can withstand soil flooding and become a problematic weed in rice (Oryza sativa L.) fields. The first comparative analysis focused on the survival and recovery characteristics of growing and mature tubers of C. rotundus exposed to soil flooding conditions. Notably, mature tubers exhibited significant survival and recovery abilities in these environments. Based on this observation, further investigation was carried out to explore the morphological structure, non-structural carbohydrates, and respiratory mechanisms of mature tubers in response to prolonged soil flooding. Over time, the mature tubers did not form aerenchyma but instead gradually accumulated lignified sclerenchyma fibers, with lignin content also increasing. After 90 days, the lignified sclerenchyma fibers and lignin contents were 4.0 and 1.1 times higher than those in no soil flooding (CK). Concurrently, soluble sugar content decreased while starch content increased, providing energy storage, and alcohol dehydrogenase (ADH) activity rose to support anaerobic respiration via alcohol fermentation. These results indicated that mature tubers survived in soil flooding conditions by adopting a “low-oxygen quiescence strategy”, which involves morphological adaptations through the development of lignified sclerenchyma fibers, increased starch reserves for energy storage, and enhanced anaerobic respiration. This mechanism likely underpins the flooding tolerance of mature C. rotundus tubers, allowing them to endure unfavorable conditions and subsequently germinate and grow once flooding subsides. This study provides a preliminary explanation of the mechanism by which mature tubers of C. rotundus from the upland areas confer flooding tolerance, shedding light on the reasons behind this weed’s increasing presence in rice fields.