Abstract: The versatility of sensors, as a crucial part of integrated devices, is receiving increasing attention. Here, a terahertz metamaterial multifunctional sensor based on the coupling of a two-layer 3D resonant structure is introduced. The sensor consists of an upper and lower polyimide film substrate, a graphite layer attached to the lower polyimide film substrate, and a periodic double-layer 3D toothed coupling resonant structure between the graphite layer and the upper polyimide film substrate, which consists of a symmetric mountain-shaped structure in the lower layer and a symmetric concave structure in the upper layer. The three-dimensional metamaterial can achieve multifunctional measurements: the refractive index change of the liquid medium can be detected with high sensitivity by measuring the resonant frequency of the structure. Therefore, it is possible to detect the liquid medium with such a design. Meanwhile, in terms of micro displacement sensing, a high micro displacement measurement sensitivity can be realized in both the z-axis and y-axis directions, respectively. The 3D metamaterial sensor proposed in this paper provides an idea for the design of a functionally integrated sensor in the terahertz region.