The cell structure and function of nitrogen-fixing cyanophytes were introduced. Chlorophyll a (Chl a) in cyanophytes possesses the capability of aerogenic photosynthesis. The heterocysts are the location of nitrogen fixation. The cells of nitrogen-fixing cyanobacteria can secrete exopolysaccharide (EPS), most of which are anion polymers and can interact with cations, EPS’s adsorption of Na+ can affect pH of external environment. The mechanism of salt tolerance of cyanobacteria were analyzed from four aspects, which focused on Na+ removal out of the cells by Na+/H+ and Na+/H+-K+ anti-carrier transportation system; pH decrease due to the acid compounds formed under the salt stress; osmatic-pressure balance of cell membrane by some soluble substances accumulated or produced and the presence of combined nitrogen, etc. The progresses of the research and application of nitrogen-fixing cyanophytes in the bio-remediation of saline-alkaline soils were reviewed. The advantages and potential of nitrogen-fixing cyanophytes in the amelioration of saline soils as well as the research and application of cyanobacteria biofertilizers were also discussed.