Despite the same crystal structure and homologous constituent elements, the chalcopyrite compounds ABTe2 (A = Cu, Ag; B = Ga, In) exhibit distinct electronic and thermal transport properties. The aim of this work is to understand the origin of such discrepancy employing experiments and theoretical calculations. The results of Hall coefficient measurements, absorption spectroscopy, and electronic transport studies suggest the deep‐level in‐gap states induced by the native A‐site vacancies play a key role in the observed intrinsic semiconductor to degenerate semiconductor transition and are the origins of the distinct electrical conductivity among ABTe2 compounds. In addition, the cryogenic heat capacity measurements and calculated phonon dispersion relations show that the acoustic and low‐frequency optical modes of AgGaTe2 and AgInTe2 are governed by the vibrations of AgTe clusters while the counterparts of CuGaTe2 and CuInTe2 compounds are dominated by the vibrations of Te atoms, and the coupling between the acoustic and low‐frequency optical modes is notably different among ABTe2 compounds. Specifically, lower avoided‐crossing frequencies, lower sound velocity together with stronger Umklapp process yield lower thermal conductivities of AgGaTe2 and AgInTe2 than CuGaTe2 and CuInTe2. This work provides new insights into the understanding and improvement of electrical and thermal properties toward higher thermoelectric performance of chalcopyrite compounds.