Abstract: Theαsubunit of phycoerythrocyanin (α-PEC) extacted from E.coli by using gene recombination technique was a kind of natural red fluorescence protein.The temperature, pH, light, and ion concentration which affected the stability of the protein were studied.Meanwhile, some metal ions and small molecules which impacted the fluorescence or UV spectrum were investigated.That proved that the temperature below 37℃ and pH between 4 and 9 could save protein better.UV radiation could destroy the structure of protein while the dark could maintain it.Ionic strength and carbohydrates had little effect on the protein, however, the majority of metal ions affected the fluorescence quenching of the protein.The work was helpful for the application of the protein used as food and cosmetics natural pigments.