For large-scale machine tools, the impact of non-rigid body behavior on volumetric error accuracy cannot be ignored, which hasn't been considered in general volumetric error model. This paper presents a comprehensive error evaluation method for large-scale gantry machine tools considering non-rigid body effect, aiming to provide guidance for volumetric error calibration process. An extended kinematic model is established based on the analysis of crosstalk influence on geometric error motions. An optimized multilateration measurement with improved accuracy and robustness is carried out for volumetric error identification, verified by Monte Carlo simulations. The main novelty of the optimization is to introduce a space uniformity index to generate specialized calibration point sets for any measurement points. A new volumetric error prediction method based on classified descriptions of geometric error motions is proposed, according to their relationship with crosstalk. Experimental results show that the proposed method achieves higher prediction accuracy in crosstalk-sensitive directions.