Impact often occurs between the stacking fork and mast of double-mast stacker crane during working process, because there is a gap between them. The operation capacity and maximum working velocity are confined due to vibrations caused by the impact. In this paper a finite element model is first obtained by using Nastran Software based on component mode synthesis theory, and modal neutral file (MNF) is also outputted in preparation for ADAMS simulation. Then a rigid-flexible virtual prototype of the stacker crane is established in ADAMS Software. In this case, the vibration response is computed by disabling those modes which cannot contribute to the deformation. Moreover, an energy trucation method is also applied in the simulation to compare the efficiency and accuracy of the two approaches. The gap size is adjusted in order to compute the vibration response of the mast and stacking fork in emergency scramming. Simulation and experiment results show that the vibro-impact simulation of the stacker crane with mode truncation by using energy criterion is more accurate and efficient, and the gap between stacking fork and mast is a major cause of its vibration. Reducing the gap can improve the stacker crane′s safety and operation capacity.