Heavy metal is a worldwide hazardous material, and many efforts were made to detect them sensitively and selectively. R-phycoerythrin (R-PE), a marine fluorescent protein, is abundant in red algae and participates in photosynthesis. In this work, the fluorescence spectroscopy and molecular mechanism of Hg²⁺ ions and R-PE were further explored through fluorescence spectrum measurements, time-resolved fluorescence lifetimes, peak fitting of Fourier transform infrared spectroscopy, and molecular docking simulation in this study. It was proved by fluorescent spectrum measurements that Hg²⁺ ions could lead to static fluorescence quenching. Besides, the interaction was a spontaneous and exothermic process driven by hydrogen bond and Van der Waals (VDW) force. Importantly, Hg²⁺ ions bound to 78LYS and 82CYS on the α chain and 73CYS and 82CYS on the β chain, which resulted in the structural changes of the peptide chain and affected the secondary structure contents of R-PE. This study further explained the effect of Hg²⁺ ions on marine fluorescent protein R-PE.