Plasmonic structure color has significant potential for visual biochemical sensing by simple instrumentation or even naked eye detection. Herein, we present a visual and real-time sensing strategy for refraction index sensing and detection of the biotin-avidin system based on three-dimensional cavity-coupled metamaterials. These metamaterials composed of a top array of gold disks, aluminium pillars and a bottom reflection film of aluminium have structures similar to the metal-insulator-metal structure. The insulating layer comprises air-gap cavities that are easily filled with gaseous or liquid dielectrics. Therefore, analytes can permeate into the nano-scale cavities and produce strong light-matter interactions. The sensor shows that any tiny change in the refraction index will induce a significant color variation and the sensitivity reaches 683.5 nm per refraction index unit with a figure of merit of 3.5. The color of the metamaterials changes from rose-red to violet and then loden after a monomolecular layer of thiolated biotin and streptavidin bind to the surface of the nanostructure successively. This sensing strategy offers new opportunities for the convenient detection of proteins, nucleic acids, and lipids.