Abstract: The flexibility of ball screws gives rise to nonlinear deviation between the measured position of the scale and the actual position of the table. To investigate the influence of ball screw on the motion characteristics of the dual-axis differential micro-feed system (DDMS), a rigid-flexible coupled dynamics model of the DDMS was constructed based on the finite element method and virtual simulation technology. The motion characteristics of the DDMS were analyzed. The results demonstrate that the elastic deformation of the screw instigates the velocity fluctuation phenomenon during the initial stage of motion at a uniform speed. During variable-speed motion, the elastic deformation exerts an influence on the velocity response of the flexible body, resulting in a phase lag between it and the rigid body. This effect is particularly pronounced at high frequencies and under variable conditions. The elastic deformation of the screw also leads to an increase in the displacement of the worktable, with an average increase of up to 1 μm. Experimental validation shows that the simulation results exhibit a high degree of consistency with the actual measured data. The virtual simulation model established in this study provides an effective theoretical analysis basis for the dynamic characteristic analysis and structural optimization of the DDMS.