A method for dynamic output force distribution of a multi-degree-of-freedom over-actuated motion stage includes: establishing a mathematical model G(s) of a motion stage based on a modal representation; setting a time delay interval parameter Δτ and an instruction shaper order nCS, and calculating each pulse time delay parameter τi; calculating matrices Tb and Vb; initializing q=1; defining Hq; calculating intermediate variable {tilde over (T)}jq, {tilde over (V)}, ΦHq, YHq, TΦHq, VΦHq, and βq; calculating an estimated value Ĥq of Hq; obtaining an amplitude Aikq of an instruction shaper; q=q+1, until calculation is completed for all logical axis channels; calculating α(s) by using Aikq; and obtaining a dynamic output force distribution matrix Tf(s). Zero-residue vibration suppression in all controllable flexible modalities can be realized with finite actuator redundancies.