[Objective] To study the fructan metabolism features of Helianthus tuberosus L. at different altitudes. [Method] “ Qingyu 2” and “Qingyu 3” Helianthus tuberosus L. were used to study fructan metabolism in each organ of Helianthus tuberosus at different altitudes. [Result] As the altitude increased, the total content of fructan in each organ decreased, so did the polymerization degree (DP) of fructan in aboveground part, fructan accumulation in tuber and transferred fructan from aboveground part to tuber. At 2 600 m or below, with the increasing altitude, the DP of fructan in tuber decreased, so did the fructan accumulation in the aboveground part; above 2 900 m, both the DP of fructan in tuber and fructan accumulation in aboveground part were high. [Conclusion] This study could provide references for expanding planting area and promoting exploitation of Helianthus tuberosus L. resources.