Clonal plants are prevalent in wetlands and play important roles in maintaining the functions of the ecosystem. In the present study, we determined the effect of clone sizes (R1, R2, and R3 comprising 1, 3, and 5clumping ramets) on the tolerance of Carex brevicuspis growing under 30-cm-deep water to three different periods (one, two, and three months) of submergence and its growth recovery one month after de-submergence. Our results showed that the relative growth rate (RGR) of C. brevicuspis significantly declined with increasing submergence time, and was higher in R3 and R5 than in R1 plants under both submergence and post-submergence conditions. The concentration of water-soluble carbohydrates (WSCs) was highest in R3, intermediate in R5, and the lowest in R1 plants during the first two months of submergence, indicating an optimal trade-off between energy investment and vegetative growth (i.e., buds and ramets production) in C. brevicuspis. WSCs were significantly reduced with increasing submergence time, while the starch content was significantly reduced only during the third month of submergence, implying that WSCs were a direct energy source for C. brevicuspis during submergence. The number of buds was higher in R5 than in R3 and R1 plants after two and three months of submergence, which directly resulted in a significantly higher post-submergence ramet production in R5 plants. These results indicated that plants with relatively larger clone sizes display better tolerance to submergence stress and post-submergence growth recovery. Therefore, we speculate that the large clone size in C brevicuspis might be an effective adaptive mechanism to survive under submergence stress in floodplain wetlands.