Different nitrogen doped amorphous carbon (CNx) films were obtained by magnetron sputtering of carbon target in argon and nitrogen atmosphere at the increasing negative bias voltages from 0 to 150 V. The films structures have experienced great change, from the novel column to nanoporous structure at the bias voltage of 0 V to the porous structure at 150 V. The proposed growth process was that the CNx nuclei grew at 0 V acted as the “seeds” for the growth of the nanocolumns, and ion etching effects at 150 V induced the formation of nanoporous structures. Furthermore, a comparison study showed that the field emission properties of the CNx films were related with the introduction of the nitrogen atoms, the size and concentration of sp² C clusters and the surface roughness. The films with rougher surface have lower threshold field.