To reduce the resonance hazard of helicopters, a fast calculation method for the vibration characteristics of helicopters when hovering in the air is needed. Under the action of centrifugal force, the natural frequency of the rotor changes under the influence of the stress stiffening effect, and there are coupling effects of rotor blades/blades and rotors/fuselage at the same time, which makes the dynamics analysis complicated. On the other hand, in order to improve the calculation efficiency, the low-order and stylization of the kinetics equation has become an urgent need. The transfer matrix method for multibody systems (MSTMM) can solve these problems at the same time. In order to accurately and quickly calculate the natural frequencies of hovering helicopters, a dynamic model of the coupling between the four flexible rotors and the helicopter fuselage was established based on MSTMM, and the dynamic topology model, total transfer equation, and characteristic equation of the system were derived. The transfer matrix of the spatial rotating beam and spinning axis was derived in detail, and the natural frequency of the hovering helicopter system could be quickly calculated. The research shows that the error between the MSTMM calculation results and the ANSYS Workbench simulation results of the spatial rotating beam was not more than 2%, and the MSTMM calculation results of the spinning axis were basically consistent with those in literature. Under the constraints of fixed tail, the first 13 order natural frequencies of the rotor/fuselage coupling system were calculated at the speed of 36.651 9 rad/s, which were consistent with the simulation results of ANSYS Workbench. When the hovering was not restricted, the first eight order natural frequencies of the hovering helicopter system were calculated, and the calculation speed was increased 7.1 times compared with the simulation speed. The results provide a new idea for helicopter dynamics analysis.