Precision glass molding (PGM) technology is a cost-efficient process for the production of micro/nanostructured glass components with complex surface geometries. The stress distribution, surface profile, and reduced refractive index of the molded lens are based on the lens being fully formed. The process of the deformation of the glass preform is rarely discussed, especially in the case of multi-machining parameters in the experiment. The finite element method (FEM) was adopted to analyze the glass preform deformation. Due to the phenomenon of incomplete deformation of the glass preforms in the experiments, two groups of finite element simulations with different boundary conditions were carried out with MSC.Marc software, to reveal the relationship between the deformation progress and the parameters settings. Based on the simulation results, a glass preform deformation model was established. The error between the model result and the simulation result was less than 0.16. The establishment method of the glass preform deformation model and the established model can be used as a reference in efficiently optimizing PGM processing parameters when the designed lens has two different base radii of curvature.