Based on the three-dimensional (3D) split-ring resonator (SRR) array and microfluidic channel, a high-sensitivity refractive index sensor based on a metamaterial (MM) absorber is realized in the terahertz (THz) band. The 3D SRR array is completely immersed in the microfluidic channel. The liquid-phase analyte in the microfluidic channel serves as the intermediate layer of the MM absorber while serving as the analyte to be measured. When the height of the microfluidic channel is fixed at 33.1 μm and the refractive index of the liquid-phase analyte injected into the microfluidic channel changes from 1.0 to 1.8, the THz MM absorber can be used as a refractive index sensor, and the refractive index frequency sensitivity reaches 379 GHz/RIU. Simulation results show that the resonant electromagnetic (EM) field of the THz MM absorber sensor is extended to 3D space, and is greatly concentrated and enhanced in the microfluidic channel, thereby realizing the spatial overlap of the resonant EM field and the analyte to be measured. The interaction between the resonant EM field and the measured analyte is enhanced, and thus the high-sensitivity sensing of liquid analytes is achieved. The influences of the height of the microfluidic channel and the thickness of the top-layer covering dielectric on the refractive index sensitivity of the MM absorber sensor are also studied based on CST Microwave Studio simulation software. In short, the THz MM absorber sensor based on the 3D SRR array and microfluidic channel has a higher quality factor and refractive index frequency sensitivity, and has potential applications in label-free fast biomedical sensing.