This paper studied the heat resistance of phycocyanin and the accumulation of phycocyanin under different light conditions in thermophilic cyanobacteria. With 30°C, 40°C, 50°C, 60°C, 65°C, 70°C, 80°C, 90°C as the experimental group, 25°C and 4°C as the control group, the placement time was set to 5 hours and 14 days. Alignments of both chain α and β were conducted to figure out the heat resistant mechanism. PKUAC-SCTE542 was cultured under different photoperiods and different combinations of light sources, and its growth and phycocyanin content were studied to explore the light conditions which were suitable for phycocyanin production. Shaking incubators with narrow band light at following wavelengths: white (400–800 nm), red (654 nm), green (511 nm), and blue (454 nm), photoperiods of 8L/16D, 12L/12D, and 16L/8D, were tested. Dry weight and content of extracted phycocyanin were measured. PKUAC-SCTE542 phycocyanin kept stable at 65°C environments, and still maintained 60% activity after being placed at 60°C for 14 days. Under the conditions of red light and photoperiod of 8L/16D, the yield of phycocyanin was the highest; while the productivity of phycocyanin was the highest when red light and photoperiod of 16L/8D were set. In result, PKUAC-SCTE542 showed great heat resistance ability in this research. With light screening done, the phycocyanin yield increased by nearly 100 mg/gDCW.