The invention relates to a glass lifter three-dimensional flexible assembly tolerance prediction method based on a finite element, and the method comprises the steps: 1, building a glass lifter dynamic simulation analysis model, and obtaining a lifting load; 2, based on the extracted lifting load, calculating the rigidity expression of the vehicle door inner plate under the action of the load, andobtaining the deformation of the upper and lower mounting surfaces of the glass lifter; 3, reconstructing lifter mounting surface characteristics according to an obtained deformation result, and establishing a three-dimensional flexible assembly tolerance model of the glass lifter; and 4, defining the ratio of the out-of-tolerance rate reduction amplitude to the tolerance reduction as the yield ratio of the tolerance reduction, and taking the yield ratio as an evaluation index to realize the tolerance optimization design of the vehicle window lifting system. According to the method, the finite element and three-dimensional tolerance design combined method is adopted, the influence of lifting loads on the assembly relation is considered, the influence of sealing resistance and the rigidityof the vehicle door inner plate on the assembly state of the lifter is revealed, the assembly relation of the glass and the sealing strip is guaranteed by optimizing tolerance design, and the liftingsmoothness is improved.