In view of the high demand on the coaxial tolerance of linear induction accelerator in centering assembling and considering the interaction among flange, bolts and gasket, finite element analysis was adopted and a 3-D finite element model of accelerator in centering assembling with bolted flange connection was built. The influence of the bolt forces on coaxial tolerance in the accelerator centering assembling was analyzed. The difference of the bolt forces in the horizontal position has more contribution to coaxial tolerance while the difference of the bolt forces in the vertical position has less so that the control of the bolt forces in the horizontal position should be imposed. The result can be used to instruct the centering assembling process to improve the coaxial tolerance of accelerator.