The modeling method of the machine tool spindle system is mostly beam and pipe element modeling. The system joint surface has two parts: The spindle and the tool holder, and the tool holder and the tool. These joint surfaces are mostly simulated by rigid connection or custom stiffness matrix. The system can also be modeled in the form of solid elements, while establishing contact pairs at the contact locations. In this paper, beam elements and solid elements were used to model the spindle system of a vertical machining center. Through the calculation results, the effects on modeling in different element types on the natural frequency of the system and the frequency response function of the tool nose point were compared and analyzed. The results show that the natural frequency value of solid element modeling is larger than that of beam element modeling, and the mode shapes are more abundant. With the increase of the excitation frequency, the amplitude?frequency response curve in the solid element modeling mode oscillates more violently, indicating that more excitation frequency values can be captured in this mode. The research results can provide theoretical reference for the dynamic characteristics of the spindle system for scientific research.