In this research, microstructure-based modeling is conducted to predict the fatigue crack nucleation life of a nickel-based alloy, Haynes 282, at different strain amplitudes from high cycle fatigue (HCF) to low cycle fatigue (LCF). A three-dimensional (3D) polycrystalline aggregate is constructed as the material representative volume element (RVE) using Voronoi tessellation with grain orientations assigned by random functions. The Hill’s yield criteria and linear strain hardening are employed to investigate the anisotropic plastic deformation in each grain using the finite element method (FEM), with the associated parameters determined by matching the monotonic stress–strain relationship and cyclic hysteresis loops of Haynes 282 alloy on the macroscopic scale. The fatigue crack nucleation life of Haynes 282 alloy is predicted using the Tanaka–Mura–Wu (TMW) model based on the material surface energy, shear modulus, Burgers vector and the plastic strain range at the microstructural level. It is demonstrated that this approach is able to predict the fatigue crack nucleation life of Haynes 282 alloy and estimate the scattering of the fatigue life by numerical simulations with different sets of grain orientation distribution functions. The results of the model prediction are in good agreement with the experimental observations. Furthermore, the effect of grain orientation on fatigue crack nucleation is discussed.