Biosensing with terahertz (THz) waves has received large amounts of attention due to its potential to detect the functional expression of biomolecules in a label-free fashion. However, many practical challenges against the diffraction limit of THz waves and the strong absorption of THz waves into polar solvents still remain in the development of compact biosensors. Here, we present a non-linear, optical, crystal-based THz-microfluidic chip with a few arrays of asymmetric meta-atoms, an elementary unit of metamaterials, for the measurement of trace amounts of solution samples. A near-field THz emission source, that is locally generated in the process of optical rectification at a fs (femtosecond) laser irradiation spot, induces a sharp Fano resonance and modifies the resonance frequency of the meta-atoms when the channel is filled with solution samples of different concentrations. Using this chip, we successfully detected minute changes in the concentration of trace amounts of mineral water and aqueous sugar solutions by monitoring the shift in the resonance frequency. A higher detectable sensitivity of 1.4 fmol of solute in a 128 pL volume of solution was achieved. This was an improvement of one order of magnitude in the sensitivity compared to our previous experiment.