C-Phycocyanin (C-PC), a spirulina-derived protein–chromophore complex, is gaining popularity in food industry because of its vivid blue color and health promoting properties that consumers crave. Also, the hierarchical protein structure and the unique light-harvesting ability render C-PC attractive for potential material and biomedical uses as photosensitizers, optical probes, and delivery vehicles. However, poor stability and techno-functionality of C-PC hindered its food applications. The material and biomedical application remains a rather blank page as there is still a lack of knowledge concerning the structural and photochemical behaviors of C-PC and its responsiveness to environmental changes. This dissertation aims to mitigate the current challenges limiting the food applications of C-PC, and then further explore potential uses of C-PC in material and biomedical areas based on its unique protein structure and light-harvesting ability. The research was conducted from both practical and fundamental aspects. Focusing on the practical issues concerning food industrial applications, the first four chapters presented multiple routes for stabilization and functionalization of C-PC. Chapters 1–2 employed complexation and encapsulation strategies to address the aggregation and color degradation problems of C-PC that occurs upon exposure to acidic pH conditions, heat, or light. Chapters 3–4 further improved the heat stability and techno-functional properties of C-PC by modifying the protein structure via glutaminase deamidation, succinylation, and PEGylation. Moving towards material and biomedical applications, chapters 5–6 investigated the structural and photochemical responses of C-PC to different environmental conditions, including pH, UV irradiation, and hydrostatic pressure. The results offered insights into the dynamic protein–chromophore interactions within C-PC and unveiled a key role of the protein structure in tuning the chromophores’ photochemical functions, including UV–vis absorption, fluorescence emission, and ROS yield. These findings enabled reversible controls on the photochemical functions of C-PC via environment-triggered protein self-assembly.