To reveal the biomass allocation response of Saccharum spontaneum Linn. at different elevations to long-term submergence in Three Gorges Reservoir, the adaptability of S. spontaneum to submergence was studied. Similar-sized seedlings of S. spontaneum with the same provenance were planted at different elevations in our study area located in the hydro-fluctuation zone of the Three Gorges reservoir region in 2008. The morphological traits and biomass of the plants were examined in 2012 and 2013. Three elevations (in the submerged area: 168 m and 172 m; non-submerged area: 176 m) were measured. The results showed that: (1) The plants at the lower elevation were shorter, and the length and basal diameter of stems at 168 m elevation were significantly lower than those at 176 m elevation (P < 0.05). The ratio of stem length to basal diameter significantly increased with decreasing elevation, while the average internode length decreased with decreasing elevation. (2) The leaf blade thickness, the ratio of leaf length to leaf width, and the ratio of leaf length to sheath length decreased with decreasing elevation, but specific leaf area increased with decreasing elevation. (3) The mass density in basal internodes showed no significant difference at different elevations after submergence (P > 0.05), although there was a significant increment with decreasing elevation before submergence. These results demonstrated that S. spontaneum could decrease the growth of seedlings, increase leaf area and sheath elongation, and increase the hyponastic growth of leaves to adapt to long-term submergence at different elevations. This suggests that the alteration of biomass allocation might be a survival strategy for S. spontaneum when exposed to long-term submergence.