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This study investigates the properties and potential applications of phycoerythrin 545, a naturally occurring light-harvesting pigment protein from Rhodomonas salina. Phycoerythrin 545, characterized by its bright red color and maximum absorption wavelength at 545 nm, was extracted using freeze–thawing methods, further purified, and analyzed using chromatographic, spectroscopic techniques, and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Phycoerythrin 545 consists of two subunits, primarily α and β, but lacks the γ subunit, and is stable at 4 °C within a pH range of 3–10. To further characterize it, its susceptibility to degradation by trypsin was assessed. The biological activity of phycoerythrin 545 and its degradation products were investigated in HT29 human colon cancer cells. The results showed that the degradation products, particularly those within 3–10 kDa, significantly decreased the viability of HT29 cells by inducing apoptosis. Mechanistic studies indicated these effects were mediated through the activation of mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinases and MAPK/c-Jun N-terminal Kinase signaling pathways and involved the regulation of key apoptotic proteins such as p53, Bim, Bad, Bak, and Bax, leading to the activation of the Caspase-3 apoptotic pathway. These findings contribute to understanding the structural and functional properties of phycoerythrin 545, laying a foundation for its exploration in food industry applications and cancer therapy supplementation.