Dynamics modeling and stress response solution of the liquid-filled pipe system (LFPS) are necessary to predict the reliability of the pipe. However, the existing methods still need further research to solve the stress response of pipe system, and the influence of fluid velocity and pressure (FVAP) fluctuations on the vibration response is not considered. Based on this, a dynamics modeling method named FEM-TMM is proposed to solve the natural characteristics and stress response of the LFPS based on the combination of the finite element method (FEM) and transfer matrix method (TMM), which can consider the fluctuations of FVAP. The incompatible solid (Solid-NC) and virtual beam (VBeam) elements are constructed to establish the finite element models of the solid and fluid domains respectively, and the coupling elements are introduced to couple the solid and fluid domains. TMM is used to solve the FVAP fluctuations of the LFPS under external excitation, and the steady-state resonant frequency and vibration mode are obtained based on the iteration method. The virtual force iteration and stress smoothing methods are adopted to solve the stress response of the LFPS, then the dynamics modeling method FEM-TMM is obtained, and the rationality of the modeling method is verified by experiments. Finally, the analysis results show that the influence of velocity fluctuation on resonance frequency and stress response can be ignored. The critical pressures of resonant frequencies are less than or equal to those of resonant frequencies without considering pressure fluctuation. There are multiple stress barriers and valleys in the different-order stress responses of the LFPS, and the pressure fluctuation will change the distribution laws and maximum peak values of the stress barriers.