Nitrogenated amorphous C (a-C:N) coatings with an intermediate sp3 C fraction of 30%–55% and N content of 0–5 at.% were deposited on single-crystal silicon wafer substrates via intermittent filtered cathode vacuum arc deposition. Some of the coated specimens were annealed at 300 and 600 °C for 4 h in a 5-Pa vacuum. The morphologies, microstructures, and the bonding structure of the specimens were characterized using scanning electron microscopy, X-ray photoelectron spectroscopy, and micro-Raman spectroscopy. The mechanical characteristics of the coatings, including the residual stress and hardness, were measured. Of the doped N content in the coatings, 60%–70% formed a pyridine- and pyrrole-like ring configuration of sp2 C = N bonds. As the N content was increased, the fraction of pyridine-like bonds decreased, and the pyrrole-like configuration gradually became dominant. Compared to the N-free coatings, the thermally stable temperature of the nitrogenated coatings decreased to approximately 300 °C, and their surface roughness increased after annealing at 600 °C. The increase in the ratio of pyridine-like to pyrrole-like bonds (Rpyd-pyr) in the coatings increased the number of voids and pinholes in the surface layer. However, the top surface of the a-C:N coating with 3.4 at.% N annealed at 600 °C remained smooth almost without voids, which could be ascribed to its suitable Rpyd-pyr and high sp2 C = C fraction.