Special recognition to molecules is essential for many biochemical processes, thus highly sensitive sensing methods for molecule recognition are strongly demanded. Recently, metamaterials present a unique platform for sensing applications owing to their exotic properties. In the current work, a metamaterial sensor for enhanced fingerprint detection of lactose based on resonant coupling of plasmonic modes of split-ring resonators (SRRs) and terahertz characteristic modes of lactose was theoretically and experimentally demonstrated. Large electric field enhancement (about 120 times) at the gap of SRRs allows for the highly sensitive detection. A narrow transmittance peak in the broader transmittance dip which corresponded to the characteristic modes of lactose was observed due to the resonant coupling, and the differential transmittance enhanced as the lactose concentration increased. The experimental result agreed well with the theoretical analysis. Moreover, the selectivity of this SRRs sensor for the target molecule was also verified by using fructose. A low amount of lactose, as small as 20 mg/mL was successfully detected in the experiment. Our study opens a new avenue to exploit new materials or devices for molecule sensing with high sensitivity and selectivity.