A high quality factor (Q-value) terahertz (THz) metamaterial sensor based on double ellipse structure is designed in this paper. Each cell of the sensor contains two 0.2 μm thick metal ellipses at a certain angle and located on the polymer substrate. The sensor structure is optimized by the finite integral time domain method, and the destruction of in-plane inversion symmetry leads to the excitation of vertically incident THz waves by the metasurface composed of the metal elliptical array. Experimental results show that the Q-value of the sensor is as high as 348. When the sensor surface is covered with a test object with a thickness of 20 μm, its sensitivity is 293 GHz/RIU (refractive index unit), and the sensor can be applied to high-sensitivity detection, trace biological sample detection, and early disease diagnosis.