The mode characteristics and the parameter sensitivity for a two-stage NGW spur planetary gear system are studied based on the principles of structure natural dynamical characteristics. Considering the influence of flexible structure including shaft, the planet carrier, and the ring-gear, the coupled lateral-torsional-axial vibration dynamical model of the planetary gear system is established under the generalized coordinate system using the shafting element method. With the model, the natural frequency and vibration mode are solved, and the results indicate that the flexibility of ring-gear has a greater effect on natural frequency. Several distinct types of vibration mode are summarized, such as planet torsional mode, sun-gear shaft axial mode, ring-gear axial mode and so on. However, the translational mode which is one of the modes in the coupled lateral-torsional lumped mass model is not found in this study. Within the scope of the time-varying, mesh stiffness mainly affects the planet torsional mode of corresponding stage. Furthermore, the variation of radial bearing stiffness will also do effect on axial vibration mode, and the variation of bearing stiffness not only affects the vibration modes of adjacent stage of planetary gear train, but also affects the nonadjacent stage. The results demonstrate the coupling characteristics of the system under the free vibration condition.