Natural Gracilaria lemaneiformis sulfated polysaccharide (GLP0, molecular weight = 622 kDa) was degraded by H2O2 to obtain seven degraded fragments, namely, GLP1, GLP2, GLP3, GLP4, GLP5, GLP6, and GLP7, with molecular weights of 106, 49.6, 10.5, 6.14, 5.06, 3.71, and 2.42 kDa, respectively. FT-IR and NMR results indicated that H2O2 degradation does not change the structure of GLP polysaccharides, whereas the content of the characteristic −OSO3H group (13.46% ± 0.10%) slightly increased than that of the natural polysaccharide (13.07%) after degradation. The repair effects of the polysaccharide fractions on oxalate-induced damaged human kidney proximal tubular epithelial cells (HK-2) were compared. When 60 μg/mL of each polysaccharide was used to repair the damaged HK-2 cells, cell viability increased and the cell morphology was restored, as determined by HE staining. The amount of lactate dehydrogenase released decreased from 16.64% in the injured group to 7.55%–13.87% in the repair groups. The SOD activity increased, and the amount of MDA released decreased. Moreover, the mitochondrial membrane potential evidently increased. All polysaccharide fractions inhibited S phase arrest through the decreased percentage of cells in the S phase and the increased percentage of cells in the G2/M phase. These results reveal that all GLP fractions exhibited repair effect on oxalate-induced damaged HK-2 cells. The repair ability is closely correlated with the molecular weight of the fractions. GLP2 with molecular weight of about 49.6 kDa exhibited the strongest repair effect, and GLP with higher or lower molecular weight than 49.6 kDa showed decreased repair ability. Our results can provide references for inhibiting the formation of kidney stones and developing original anti-stone polysaccharide drugs.