The objective of the study is to characterise the taxonomy of the thermophilic filamentous strain B121 isolated from the hot springs in Ganzi, Sichuan, and provide insight into its genetic basis for future application. The taxonomy of strain B121 was analyzed by using polyphasic approach encompassing genome analysis, phylogenetic analysis, secondary structure prediction, and overall analysis of morphology, sodium salt tolerance test combined nitrogen fixation ability. Phylogenetic analysis of 16S rRNA indicated that strain B121 closely clustered with strains Thermoleptolyngbya oregonensis PCC 8501, Thermoleptolyngbya albertanoae ETS-08 and Thermoleptolyngbya sp.O-77; the 16S-23S ITS secondary structure prediction showed that the D1-D1' region of strain B121 has certain similarity and high sequence identity with reference strains, but they have not reached the generalized threshold for the same species. Additionally, the secondary structures of V2, BoxB and V3 regions are quite different between B121 and other reference strains. Combined with the analysis of morphological investigation, strain B121 was identified as a new species of the genus Thermoleptolyngbya. In addition, the strain B121 can survive in NaCl and NaNO3 modified BG-11 medium with a concentration of 0.5 M, and it can also survive in NaCl modified BG-11 medium with a concentration of 1 M. When the gas phase condition is Ar:N₂:CO₂ = 79:20:1 (v:v:v), the acetylene reduction rate of strain B121 can reach 2564.1 nmol/(g·h).