Surface-enhanced electromagnetic response in the resonant regions of split-ring resonators offers a sensitive way to probe the surface dipoles formed by alkanethiol molecules with a terahertz wave by a differential transmission (DT) interrogation method. The DT signal mainly comes from the interaction between alkanethiols and metamaterials by electron transfer and/or the variation of the dielectric constant. The Lorentz model is used to demonstrate the principle of DT interrogation theoretically, which suggests the variation of both frequency and damping of resonance can be captured cooperatively. This method has been employed to experimentally demonstrate the sensing feasibility for the chain length dependence of the alkanethiol molecules. Numerical simulations confirm that the enhancement is large at the gap and corner regions of this kind of metamaterials.