Abstract: Take the Dragon-Ⅰ accelerator as an example, the structure response under strong vibration has been calculated using time history analysis method for the large scale accelerator, and the offsets of key points on the accelerator were measured. Numerical results show that there is 2 mm deformation in the middle of the accelerator, and in this segment the measured alignment offset is about 0.6 mm, and the measured displacement is about 2 mm. Based on the analysis of numerical calculation and measurement, the linear deviation of mechanical axis is less than ±0.2 mm after alignment. The analysis show that the calculation results can provide references for measuring point arrangement, on-site inspection and measurement data analysis.