In this study, the light factors and nitrogen availability effect on Thermosynechococcus sp. CL-1 (TCL-1) productivity of biomass and C-phycocyanin were observed. The variation of light factors (intensity, color and arrangement) and concentration of dissolved inorganic nitrogen (DIN) from 2.9 to 116.7 mM were applied in the TCL-1 cultivation with 3 g/L initial biomass concentration. Moreover, extended cultivation using two DIN concentrations with better results and various lighting arrangements were conducted. Additionally, the malondialdehyde (MDA) content in the biomass was also measured as the indicator of oxidative stress. The double-side lighting arrangement with the intensity of 500 and 1000 μmole m−2 s-1 reach better biomass productivity while the mixed lighting with red LED enhances C-phycocyanin productivity. Outstanding C-phycocyanin productivity of 281.4 ± 10 mg L-1 day-1 is achieved by the application of double side mixed color lighting and the intensity of 250 μmole m−2 s-1 on each side. Application of 2.9 mM DIN in the TCL-1 culture gains the highest biomass productivity recorded as 2022 ± 162 mg L-1day-1. Otherwise, highest C-phycocyanin productivity is 201.6 ± 40.4 mg L-1day-1 with 14.6 mM DIN. The higher concentration of MDA, which indicates the larger amount of free radical in the FPBR, is produced in the cultivation using 2.9 mM DIN.