© 2020 Wiley Publishing Ltd. Contact fatigue is a key feature limiting the service lives and reliabilities of gears. The gear contact fatigue failure mechanism has not been understood fundamentally due to the complexities of structural factors, material properties, and operating conditions. In this work, an integrated finite element model of a megawatt level wind turbine gear is established considering the real gear geometry, material microstructure heterogeneity, existence of nonmetallic inclusion, and the tooth surface roughness. The gear steel material properties are defined based on the crystal elasticity anisotropy framework. The modified Dang Van multiaxial criterion is utilized to estimate the material fatigue failure probability during gear engagement. With the developed model, the roles of microstructure, inclusion, and surface roughness on the gear contact fatigue behaviour are comparatively investigated. Additionally, the influences of different inclusion size and surface roughness profile on gear failure risk are investigated and discussed in detail.