In this paper, a new version of the Stillinger–Weber (SW) potential for wurtzite GaN is presented, by which we systematically explore the structural and thermodynamical properties of native point defects and their complexes. In parallel, the semi-empirical Modified Embedded-Atom Method (MEAM) potential is selected for comparison. The SW and MEAM potentials are assessed by the reproduction of the fundamental properties of wurtzite GaN and by the ability to describe the inversion domain boundaries and the wurtzite–rocksalt phase transition. Then the structural search of native point defects and their complexes in GaN is implemented using both SW and MEAM potentials with the benchmark of Density Functional Theory (DFT) calculations. Besides vacancies and antisites, four N and five Ga interstitials are confirmed by refining the DFT calculations, among which two N split interstitials [Formula: see text] and [Formula: see text], and two Ga split interstitials, [Formula: see text] and [Formula: see text], are observed for the first time. The SW potential correctly predicts the octahedral occupation GaOct to be the most stable Ga interstitial, while the MEAM potential predicts the ground state of the [Formula: see text] split interstitial [Formula: see text] as the most stable N interstitial. However, neither of the two potentials could simultaneously generate the most stable configurations of N and Ga interstitials. The investigations of point defect complexes reveal that N octahedral Frenkel [FrenkelOct(N)] and paired antisite (NGaGaN) defects are unstable and get converted into [Formula: see text] configurations with different separations between VN and [Formula: see text] point defects based on the DFT calculations. The formation energies calculated by the DFT and SW potential demonstrate that Schottky, Ga octahedral Frenkel [FrenkelOct(Ga)], and [Formula: see text] point defect complexes are energetically feasible and that they should not dissociate into two isolated point defects. In contrast, the MEAM potential predicts the dissociation to be exothermic for Schottky and [Formula: see text]. Overall, the structural features concerned with N–N or Ga–Ga bonds relaxed by the SW potential are more consistent with DFT calculations than the MEAM counterpart.