Herein, we have shown that the phase composition of molybdenum carbide catalysts has a pronounced effect on the pairwise hydrogen addition selectivity in the gas-phase propyne hydrogenation with parahydrogen. Molybdenum carbide catalysts were prepared using either the Pechini method or temperature-programmed reduction with CH4/H2 carburizing gas mixture. The structures of carbide catalysts were characterized by high-resolution transmission electron microscopy, X-ray diffraction, and X-ray photoelectron spectroscopy. It was found that molybdenum carbide prepared by the Pechini method predominantly contains a face-centered-cubic MoC1−x phase, while the TPR method yields a hexagonal-close-packed Mo2C phase. By varying the gas hourly space velocity of carburizing gas mixture, the defected phase can be produced. Computer modeling for XRD patterns was used to identify the phase composition of Mo2C catalysts. All the catalysts were found to be active in pairwise hydrogen addition; however the hcp-Mo2C phase exhibits a higher contribution of pairwise H2 addition providing ~ 150-fold proton NMR signal enhancement.