Cratonic lithosphere is a vast host for deep recycled carbon, trapping up to several weight percent CO2 among its compositions1,2 at depths overlapping the seismic mid-lithospheric discontinuities (MLDs)3-5. However, the role of carbonates, especially for the latest discovered amorphous calcium carbonate (CaCO3)6, is underestimated in forming MLDs. Using the pulse-echo-overlap method in a Paris-Edinburgh press coupled with X-ray diffraction, we explored the acoustic velocities of CaCO3 under high pressure-temperature (P-T) conditions relevant to the cratonic lithosphere. Two anomalous velocity drops were observed associated with the phase transition from aragonite to amorphous phase as well as with pressure-induced velocity drop in amorphous phase around 3 GPa, respectively. Both drops are comparable with approximately 35% and 52% reductions for compressional (VP) and shear (VS) wave velocities, respectively. The VP and VS values of the amorphous CaCO3 above 3 GPa are about 1/2 and 1/3 of those of the major upper-mantle minerals, respectively, and they are the same with aragonite below 3 GPa. These velocity reduction by the presence of CaCO3 would readily cause MLDs at depths of 70–120 km dependent on the geotherm even if only 1-2 vol.% CaCO3 presents in the cratonic lithosphere. The CaCO3-originated MLDs is weak so as to be expected to influence the stability, rifting, and delamination of the craton7.