Employing the first-principles simulation combined with the statistical model, we have investigated the interplay between impurity of nitrogen (N) and vacancy in molybdenum (Mo). Single N atom is energetically favorable occupying the octahedral interstitial site. N atom can be found to easily bond at vacancy, and the trapping energy of N trapped by vacancy is 2.71 eV, in good agreement with the experimental result. Further, we predict vacancy concentration in the form of N1V complex in Mo, which notablely increases due to the presence of N, despite the concentration of interstitial N is still higher than that of N1V complexes. The results demonstrate the key role of vacancy on N trapping in Mo.