Based on RCSA, this paper predicted the frequency response function of the endpoint of a deep hole internal grinder spindle. At first, the method separated the model of grinder spindle into several subsections to calculate their free-state frequency response function (FRF) matrices, then rigidly coupled the FRF matrices of each substructure sequentially, revised the FRF matrices of the coupled substructure with structural modification method at the support points of bearings, coupled till to the last substructure, then the FRF of the endpoint of grinder spindle was calculated.With a deep hole internal grinder spindle system as the research object, the paper predicted the FRF of the spindle endpoint through proposed method and finite element method, meanwhile a group of FRF data were collected by experiments.Experimental results indicate that this method, with higher prediction precision and faster calculation speed, is better in the structure optimization of the deep hole internal grinder spindle system.