A new type of FT pin-cycloid transmission reducer is widely used in the industrial robot field due to the high transmission accuracy. In addition, the complex working conditions bring about vibration, which affects the transmission accuracy of the robot. Therefore, it is necessary to study the dynamic characteristics of FT reducer at the transmission joint. In this paper, based on the analysis of its transmission principle and structure, the dynamic model of FT transmission is established by necessary assumptions. The stiffness mathematical models of different meshing positions are obtained from the dynamic model, and the differential equations of the system are established by Lagrange method. In order to solve the natural frequency of the system, the stiffness of meshing positions of the system is solved, including input shaft torsional stiffness, involute gear meshing stiffness, bearing stiffness, cycloid gear and pin torsional stiffness. Considering the output of FT transmission, a “3+ i” model is proposed to obtain the mesh stiffness between the cycloid gear and output pins. Finally, the correctness of the model is proved by choosing parameters such as transmission ratio and force on parts and components by simulation. The research results will provide theoretical support for the optimal design of FT transmission.