We present the design of an innovative dual-band terahertz sensor based on a metamaterial array and a microfluidic channel. The sensing performance of two ultra-high absorption peaks—with absorption rates of 99.96% and 99.85%—generated in the frequency band of 0.2 to 1.2 THz is analyzed. Refractive indexes of analytes are predicted to be in a specific refractive index range, demonstrating the very low prediction error rate of the proposed sensor. Further analyses show that the designed sensor has application potential in label-free and rapid detection.