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Under deep-water test conditions, a riser-test pipe system (RTS) is subject to the vortex-induced effect on the riser, flow-induced effect on the test pipe, and longitudinal–transverse coupling effect. Further, the system is prone to buckling deformation, fatigue fracture, and friction perforation. A three-dimensional (3D) nonlinear vibration model of deep-water RTS was established using the micro-finite method, energy method, and Hamilton variational principle. Based on the elastic–plastic contact collision theory, a nonlinear contact load calculation method between the riser and test pipe was proposed. According to field parameters in the South China Sea and the similarity principle, a vibration test bench for the RTS was designed. The experimental measurement results and the calculation results obtained from the proposed vibration model and the single tubing vibration model developed in our recent study were compared. Based on this comparison, the correctness and effectiveness of the proposed vibration model of the deep-water RTS were verified. Then, the vibration characteristics of the RTS for the BY5-2-1 well in the South China Sea were analysed. The results demonstrate that, first, in the vibration fatigue analysis of the test pipe, the influence of its own local high-frequency vibration cannot be neglected. Second, long-term collisions will cause friction and wear failure in the RTS. In the safety analysis of the RTS, the wear problem of the RTS caused by the collision between the riser and test pipe cannot be neglected. Third, the position where the test pipe is prone to strength failure is mainly located in the upper and lower parts. The field designer should focus on the safety of the pipe at these locations. • A three-dimensional nonlinear vibration model of deep-water riser-test pipe system is established. • A nonlinear contact load calculation method between the riser and test pipe is proposed. • A similar experiment of RTS vibration is designed and completed to test the validity of vibration model. • The vibration characteristics of the RTS for the BY5-2-1 well in the South China Sea are analysed. [ABSTRACT FROM AUTHOR]