A thermophilic cyanobacterium named Thermosynechococcus CL–1 (TCL–1) was cultivated in the flat plate photobioreactors under strong illumination with dense culture to examine the effects of nutrient concentrations on the biomass production, CO2 fixation, and the potential as the feedstock for bioethanol production. The results show that concentrations of Na+, NO3–, and CaCl2•2H2O, should be decreased, but the MgSO4•7H2O concentrations should be enhanced to increase the biomass productivity or persistence of the growth. Most of the carbon contents in TCL–1 remain stable, about 40%, under various nutrient levels. In addition, the Su and Chu’s medium was reorganized by picking up the nutrient concentrations resulted in the great biomass production. The adoption of the new medium for cultivating TCL–1 exhibits the great biomass productivity, CO2 fixation rate, and glycogen productivity at 138.7, 221.5, and 75.9 mg L–1 h–1, respectively, under 2,000 µE m–2 s–1 illumination in the 1.5 cm light path flat plate photobioreactors. The high biomass productivity, CO2 fixation and glycogen productivity indicate the use of Su and Chu’s medium exhibits high potential for applying TCL–1 in CO2 fixation and bioethanol production potential in the flat plate phptobioreactors.