Molybdenum nitrides and their related compounds have been focused as a catalyst for several reactions. Although the doping into molybdenum nitrides lead to the higher catalytic activity, the simultaneous control of the morphology, the crystallinity, and the dopant state in doped MoN cannot be easily achieved due to the limitation of the synthesis method. In this study, one of the mixed anion compounds, NaMoO3F was used as a precursor for molybdenum oxynitrides with hexagonal MoN phase. This route led to the homogeneous distribution of cobalt in the molybdenum oxynitride compared with that obtained by the other method. The cobalt-doped molybdenum oxynitride from NaMoO3F exhibited high oxygen reduction reaction catalytic activity due to the high distribution of cobalt in the crystal. This paper proposes that the mixed anion compounds can be a unique precursor for the other materials to expand the controllability of materials toward improvement of their activity.