GaN with atom defects is a rising material platform for single‐photon emitter (SPE) recently due to their room‐temperature working conditions, high emission rate, narrow emission line‐width and mature processing technology. However, the SPE mechanism still remains unclear to date, which greatly hinders the progress of GaN based SPE. Herein, systematic ab initio calculations predict and identify two kinds of intrinsic point defects NGa and NGaVN in GaN, which can be response for the widely observed SPEs. The formation energy, band structure, transition mechanism, and orbital composition are systematically investigated. The results indicate that NGaVN° possesses a large zero‐phonon line (ZPL) of 1.98 eV and a short lifetime of 3.56 ns, which may be one of the most possible origins of SPEs in visible wavelengths. The calculation results coincide well with our measured ZPL (1.92 eV) and lifetime (1.14 ns), as well as the experimental results reported previously. This work also predicts that NGa0 and NGaVN+1 can produce SPEs at fiber telecommunications band (0.84 and 0.94 eV, respectively). These results give deep insights into the SPE emission mechanism in GaN and bridge the gap between the realized SPEs and the underlying physical mechanism.