Geometrical discontinuities are inevitable in engineering structures due to various functional requirements, which often yield complex stress–strain state and thereby significantly impact their fatigue performances. In this study, crystal plasticity theory is coupled with traditional critical distance theory for notch effect modelling considering microstructural heterogeneity. Specifically, microstructural and geometrical size effects on critical distance and fatigue performance are studied based on Sub-modelling approach. In addition, critical distance theory is coupled with Weibull distribution for probabilistic fatigue life evaluation of notched components. The developed method is verified and compared by using experimental data of GH4169 alloy. The findings demonstrate that the evaluated P-S-N curves exhibit strong agreement with tested data and geometrical size effect poses larger influence than the grain size effect on critical distance and fatigue life.