A three-dimensional(3D) line-contact mixed lubrication model and contact fatigue life prediction model for gears are established, considering the elastoplastic contact of ellipsoidal asperities and their interactions. The localized lubrication states across the actual 3D rough surfaces are visually depicted. The direct asperity contact pressures calculation exhibits greater accuracy and universality. The proposed mixed lubrication model can be applied accurately and efficiently to heavy-load conditions. The synergistic mechanisms of multi-scale surface integrity parameters, such as surface morphology-lubrication coupling, hardness gradient, and residual stress, on gear contact fatigue has been revealed. The results reveal that surface roughness significantly affects the competitive failure mechanism between surface-initiated micropitting and subsurface-initiated macropitting. The increase in surface compressive residual stress is more sensitive to the enhancement of near-surface and subsurface fatigue lives, compared to the increase of peak residual stress and the depth of peak residual stress. The proposed physics-based gear contact fatigue life prediction model has been validated through gear contact fatigue experiments under various operating conditions. The maximum deviation between the predicted and experimental fatigue lives is within 10%. This paper presents theoretical methodologies and data-driven support for optimizing the design and manufacturing processes of gears, specifically focusing on enhancing anti-fatigue properties.