One embodiment of the present invention provides a system that accurately predicts an apodization effect in an optical lithography system for manufacturing an integrated circuit. During operation, the system starts by collecting an apodization-effect-induced spatial transmission profile from the optical lithography system. The system then constructs an apodization model based on the spatial transmission profile. Next, the system enhances a lithography model for the optical lithography system by incorporating the apodization model into the lithography model, wherein the enhanced lithography model accurately predicts the effects of apodization on the optical lithography system.