Quantification of natural carbonate minerals, namely, aragonite, high- and low-Mg calcite, and dolomite provides essential information about biomineralization, carbon cycling on Earth, and the evolution of ocean chemistry, and is also useful in many other scientific, pharmaceutical, and industrial fields. However, X-ray diffractometer has previously been the only practical tool to identify and quantify carbonate minerals, including calcium carbonate (CaCO3) polymorphs. We propose new fingerprint terahertz (THz) absorption and reflective index spectra in the 1-6 THz range that probe the lattice phonon modes and can be used for sensitive quantification of these four carbonate minerals, including polymorphs. In THz time-domain spectroscopy with our unique attenuated total reflection system, high- and low-Mg calcite and aragonite show different absorbance and reflective index amplitudes at 3.32 THz, which corresponds to the transverse optic mode. Dolomite shows a distinct absorbance peak and reflective index at 4.82 THz because its space group (R3̅) is different from that of calcite (R3̅c). THz absorbance and reflective index curves of the mixed carbonate materials, which typically occur in natural environments, correspond well to the curves calculated from the results of single-mineral samples (R 2 > 0.98). Remarkably, the absorbance and reflective index can quantify small fractions (<1%) of low-Mg calcite in an aragonite matrix with high linearity (R 2 = 0.99). Our findings provide a new method for screening low-Mg calcite diagenetic overprints on primary aragonitic skeletons such as corals, which is crucial for climate reconstructions using the isotopic analyses because a 1% overprint can cause estimated temperature deviations of ∼1 °C. THz spectra of carbonate minerals offer not only a new high-sensitivity quantification tool for interdisciplinary fields, but also safer light-source handling than X-ray diffractometer.