Carbon nitride nanocrystals were synthesized on Co/Ni-covered Si(100) wafers using a nitrogen-atom-beam-assisted pulsed laser ablation deposition method. Transmission electron miscroscopy, x-ray diffraction, and Raman spectroscopy showed that as-deposited films were constructed primarily from nanometer-sized β-C3N4 and CNx crystallites. The co-catalyzation by the cobalt and nickel in the synthesis process is considered to play an important role in the formation of nanocrystalline β-C3N4. The reasons for the formation of carbon nitride nanocrystals were analyzed.