Molybdenum nitrides were prepared by temperature-programmed reduction of MoO3 with flowing NH3. They were tested for indole HDN and benzothiophene HDS. Too low or high NH3 space velocity was inadequate to produce high surface area Mo nitride. The temperature ramping rate (except the rate higher than 2.5 K/min in β1 temperature range) hardly affected the surface area of the prepared samples. The XRD analysis suggested that MoO2 was the important intermediate for producing the high surface area Mo nitride. The catalytic conversions of Mo nitrides for indole HDN and benzothiophene HDS were well correlated with their surface areas. The reaction pathways of both reactions were proposed. The Mo nitride could be an effective catalyst without further hydrogenation of aromatics, thereby reducing the consumption of hydrogen.