Abstract: This paper aimed to study the extraction and purification of phycocyanin from Synechococcus sp. PCC7002 (hereinafter referred to as “Synechococcus”) and its heat-induced fading mechanism. Phycocyanin was extracted and purified through high-pressure homogenization, chitosan flocculation and ammonium sulfate salting out. And its fading mechanism during heat treatment (50 ℃, 60 ℃, 70 ℃, 80 ℃, 90 ℃, 30 min) was studied by color index, UV-Vis spectrum, fluorescence emission spectrum, particle size and potential, FTIR spectrum and SDS-PAGE electrophoresis. The results showed that optimal extraction conditions of phycocyanin were to dissolve algal power in 0.04 mol/L NaCl solution to make the concentration reach 2 mg/mL and homogenize it at 80 MPa for 7 min, and the resulting yield of phycocyanin was 10.5081%±0.0936%. After flocculation by 0.15 mg/mL chitosan and salting out by 50% saturated ammonium sulfate, phycocyanin purity could be increased from 0.6950 ± 0.0043 to 1.9084±0.2621. Further research on thermal-induced fading mechanism of phycocyanin found: Destruction of spatial structure of the apoprotein started from 60 ℃, which led to transformation of natural conformation of phycocyanobilin chromophore maintained by protein backbone and a significant decrease in ultraviolet absorption and characteristic fluorescence of phycocyanin, therefore blue hue of phycocyanin was greatly destroyed. Particle size results indicated that phycocyanin molecules began to aggregate at 60 ℃, while larger aggregates formed at 80 ℃ may lead tetrapyrrole chromophore to be buried in it, deepening fading degree of phycocyanin color. In addition, FTIR spectroscopy and SDS-PAGE indicated that β subunit of phycocyanin was probably damaged more serious than α subunit during heat treatment, and the damaged structure were mainly α-helix. In summary, maintaining structural stability of apoprotein or protein segment near the phycocyanin chromophore was the key factor of keeping phycocyanin tone stable during the heat treatment. This research would provide certain theoretical basis for the study of phycocyanin color protection technology during the heat treatment process.