This paper presents a three-dimensional vortex-induced vibration prediction model for a long flexible riser under linearly sheared currents. Two distributed and coupled van der Pol wake oscillators are utilized to characterize the fluctuating lift and drag coefficients, respectively. It should be noted that geometric and hydrodynamic nonlinearities are also considered in our model. Numerical simulations by finite element method are carried out to solve the highly coupled nonlinear fluid–structure interaction equations. Firstly, modal analysis is performed to obtain the foremost ten natural frequencies of the flexible riser under top-end tension by theoretical and numerical methods, and the results agree very well. Then, nonlinear dynamic analyses are carried out to investigate the effects of linear shear flow on displacements, stresses, modal variations and phase portraits. The results obtained in uniform and linear shear currents are compared in detail. The results indicate that the asymmetric phenomenon along the riser span is more obvious with increasing linear shear velocity and the lock-in phenomenon of IL (in-line) response frequencies with multi-frequency is also observed along riser span. Moreover, it is also revealed that the dynamic responses simultaneously exhibit the standing and travelling wave patterns under linearly sheared currents, and the dynamic responses become more irregular than uniform flow.