In this research, we computationally analyzed the structural modes of an HSK63E type tool system and verified the results with experimental modal analysis (EMA). The computation was implemented using the finite element method (FEM) based on a linear-elastic theory, with which we computed the natural frequency and obtained the modal shapes under both free and operating conditions. With the method of experimental modal analysis, we also obtained structural modal parameters including the natural frequency, modal shapes and damping ratio under the same free and operating conditions. The computational data were compared with the experimental findings. The reasonable agreement between the two data sets indicated the validity and provided a theoretical basis for using computational methods for determining the natural characteristics and influencing factors of HSK tool system. With this validated FEM model, further analyses were performed to evaluate the unique dynamic performance of the HSK tool system, and to apply dynamic optimum design to other types of HSK tool system.