In order to understand the effects of sugar metabolism on drought resistance in wheat, two wheat cultivars with different levels of drought resistance were used in this study. We investigated the accumulation pattern of water-soluble carbohydrates (WSC) and expression profiles of twelve fructan metabolism-related genes in peduncle (PED), penultimate (PEN), and lower internode (LOW) stem tissues under drought stress. LH7, a higher drought-resistance cultivar, contained a higher stem dry weight and higher content of WSC in PED, PEN, and LOW tissues, while XN979, a lower drought-resistance cultivar, contained lower values. The tissues from LOW internodes had the highest WSC content, while PED had the lowest. The mRNA levels of genes encoding fructan synthesis-related enzymes, sucrose: sucrose 1-fructosyltransferase (1-SST), sucrose: fructan 6-fructosyltransferase (6-SFT), and fructan: fructan 1- fructosyltransferase (1-FFT) showed higher expression levels at early time points following stress, whilst the genes encoding degradation-related enzymes, fructan exohydrolases (1-FEH), and invertase (INV), showed higher expression at a later time point. Compared with XN979, LH7 showed higher expression levels of genes encoding fructan synthesis-related enzymes at all growth stages, whilst the expression of 1-FEH-W3, 6-FEH, and INV3 were higher at a later stage; these expression levels would benefit fructan accumulation and remobilization at early and later stages, respectively. Drought stress induced most of fructan metabolism related genes expression level decreasing in LH7 PED, but enhancing in LH7 LOW part at early time points following stress. The results confirm that there are complex, coordinated expression patterns of fructan synthesis- and degradation-related genes in stems under drought stress. In summary, 1-SST-A2, 6-SFT, 1-FFT-A, 1-FEH-W3, 6-FEH, and INV3 play important roles in fructan accumulation. In addition, higher expression of genes related to fructan synthesis and degradation occurs during early and later stages of drought stress, respectively, enhancing the drought resistance of wheat cultivar LH7.