In this study, multispectral analysis and molecular simulations were performed to investigate the interaction mechanism between phycocyanin (PC) and lysozyme (Lys). The interaction was examined using surface plasmon resonance (SPR), and the structural changes were analyzed using Fourier transform infrared (FTIR) spectroscopy, X-ray diffraction (XRD), and transmission electron microscopy (TEM). The results suggest that the interaction between PC and Lys was primarily driven by electrostatic, hydrophobic, and hydrogen bonding forces. Molecular dynamics (MD) simulation revealed that Lys preferentially binds between the two subunits, alpha (α) and beta (β), of PC, with residues ASP-13, GLU-106, and GLU-115 on PC and ARG-119, ARG-107, and ARG-98 on Lys being the main contributors to the binding interaction. Additionally, the formation of the PC-Lys complex resulted in increased kinetic and improved thermal stability of PC, which have important implications for PC applications.