The remarkable increase in the complexity and size of spacecraft has inflicted unprecedented difficulties and challenges on system level dynamics simulation. At present, dynamic substructure method is mainly adopted to improve the solution efficiency and protect the proprietary technologies in model sharing among different project groups. The acceleration shock response spectrum is commonly used to describe the impact dynamic environment during the soft landing phase. It is acknowledged that the effects of high order modes on acceleration responses are more significant than those on displacement responses, so under the condition of small damping, the acceleration prediction accuracy is far lower than the prediction accuracy of displacement obtained by classical substructure methods based on modal with identical cut-off frequency. To solve this problem, a recently proposed novel method called impulse based substructuring (IBS) method is applied and its reduced-order form of iterative solution format used to predict acceleration is presented. Based on the buffer load measured from the soft landing numerical experiment, the acceleration response of the lunar lander is respectively calculated through the Craig-Bampton (CB) method and the IBS method. A numerical example shows that the IBS method has higher accuracy and efficiency than CB method, and it is suitable for rapid prediction for acceleration of the lunar lander with high accuracy.