The sensitivity of plasmonic nanostructures based refractive index sensor can be improved by free-standing three-dimensional (3D) configuration. Here, by means of focused-ion-beam (FIB) induced folding technique, we fabricated arbitrary spatially oriented double-flake 3D metamaterials (MMs). The experimental measured sensitivity can reach 2703 nm/RIU, and based on the symmetry breaking configuration, the figure of merit (FoM) reaches 37.2 RIU −1 in simulation results. What's more, the different coupling mechanisms in our MMs enable the independent modulation of each resonance. This work opens up new avenues for near-field coupling modulation, holding great potential applications in multi-resonance differential sensing, switch devices and optical communication. • The sensitivity of plasmonic nanostructures based refractive index sensor can be improved by free-standing three-dimensional configuration. • The measured sensitivity can reach 2703 nm/RIU. • Based on the symmetry breaking configuration, the figure of merit reaches 37.2 RIU-1. • Each resonance can be modulated independently.