Color centers are vital for quantum information processing, yet traditional ones often face challenges in fabrication, location, and stability. Realizing color centers in natural intrinsic defects will overcome these challenges. Here, $g-{\mathrm{C}}_3{\mathrm{N}}_4$ with natural intrinsic vacancies is identified as an excellent candidate for trapping B/C atoms to form stable color centers as qubits. B/C atoms are expected to be precisely placed at identifiable vacancies in $g-{\mathrm{C}}_3{\mathrm{N}}_4$ through scanning tunneling microscope manipulation. The vacancy sites are confirmed as the most stable adsorption positions protected by diffusion barriers from thermal diffusions. The most stable charge states are ${\mathrm{C}}_{\mathrm{V}}^{+2}/{\mathrm{B}}_{\mathrm{V}}^{+2}, {\mathrm{C}}_{\mathrm{V}}^{+1}/{\mathrm{B}}_{\mathrm{V}}^{+1}$, and ${\mathrm{C}}_{\mathrm{V}}/{\mathrm{B}}_{\mathrm{V}}$ in turn, with charge transition levels of 0.39 and 2.49 eV, respectively. Specifically, the defect levels and net spin of ${\mathrm{C}}_{\mathrm{V}}/{\mathrm{B}}_{\mathrm{V}}$ can be adjusted by charge states. The zero-phonon line (ZPL) of ${\mathrm{C}}_{\mathrm{V}}$ is 1.95 eV, close to that of the $\mathrm{N}{\mathrm{V}}^{-}$ centers in diamond, while the ZPLs of ${\mathrm{C}}_{\mathrm{V}}^{+1}, {\mathrm{C}}_{\mathrm{V}}^{+2}, {\mathrm{B}}_{\mathrm{V}}^{+1}$, and ${\mathrm{B}}_{\mathrm{V}}^{+2}$ fall within the near-infrared range, making them ideal for stable initialization and readout. The larger Debye-Waller factors (from 0.1 to 0.36) indicate sufficiently strong coherence. Furthermore, the zero-field splitting parameter and the characteristic hyperfine tensor are provided as potential fingerprints for electron paramagnetic resonance experiments.

• Color centers
• Point defects
• 2-dimensional systems
• Qubits
• First-principles calculations