In order to study the function of HSF transcription factor in Tartary buckwheat, a HSF family gene was cloned from ‘Chuanqiao No.1’ in this study. The open reading frame is 1047 bp in length encoding for 349 amino acids. The analysis of gene structure showed that FtHSFA6b gene is composed of two exons and one intron. The sequence alignment and phylogenetic analysis showed that FtHSFA6b protein was closely related to CQA-2C in Chenopodium quinoa and GHA-7A in Gossypium hirsutum. Cis-acting elements in the promoter of FtHSFA6b were predicted and divided into five categories. Furthermore, tissue-specific expression analysis showed that FtHSFA6b gene was expressed in roots and leaves, with the lowest expression in roots and the highest expression in stems. qRT-PCR showed that the expression of FtHSFA6b was induced under MeJA or NaCl treatments. The analysis of total flavonoids content in transgenic hairy roots showed that the overexpression of FtHSFA6b could increase the tolerance of hairy roots to salt treatment, and the total flavonoids content also increased significantly. In transgenic Arabidopsis thaliana, over-expressing FtHSFA6b can improve the salt tolerance at the germination stage, possibly by decreasing malondialdehyde (MDA) content and increasing the activities of Catalase (CAT) and peroxidase (POD).