This article presents an approach to investigate the variation propagation of machine tools due to the geometric errors produced in assembly process and determine a pre-adjustment method in assembly design stage. At the beginning, a state-space model was used to describe the variation propagation in machine tool assembly process. Subsequently, a finite element analysis consistent with a selected assembly sequence was conducted, including the components in their unassembled state which is always ignored in the existing study. A horizontal machine center was taken as an example to clarify the proposed method. The guide rail deformations in normal direction were defined to obtain the joint kinematic errors in each assembly station. Based on this, an analysis calculation is formulated to determine the total deviation in assembly and then the adjustment before assembling was identified to reduce the assembly errors. The method has strong feasibility and practicality, and when this method is adopted, the static deformation error produced in assembly process would be decreased obviously and can effectively improve the precision of machine tools assembly. The proposed method was eventually applied to the assembly of a horizontal machine center, and the final evaluation of accuracy in our experiments can meet the requirements well.