The gears in aviation gear systems are susceptible to fatigue fracture due to high-speed, heavy-load, and load alternation operating conditions. Therefore, a numerical calculation model with multiple mesh positions loading form has been proposed in this paper to analyze the fatigue crack initiation and propagation behavior, and to estimate the fatigue life of these gears. The fatigue life of the gear is determined by separately calculating the fatigue crack initiation life and the fatigue crack propagation life. The tooth root fatigue stress and the fatigue initiation life are calculated by the multi-axial fatigue life prediction method with the Smith-Watson-Topper criterion and the critical plane method. Afterwards, the tooth root stress–strain field is calculated in Finite element (FE) software and the stress intensity factors of the crack tip are calculated in three-dimensional (3D) crack analysis software. Then, the tooth root fatigue crack propagation trajectory and the fatigue crack propagation life are obtained separately. Finally, the influence mechanism of the loading conditions, the geometry parameters of gears, and the initial crack positions on the tooth root fatigue crack initiation life, propagation life, and fatigue crack propagation trajectory are analyzed, and a tooth fatigue test bench is built for verifying the crack propagation trajectory.