In this article, a vortex-induced vibration prediction model of a flexible riser conveying two-phase flow, including geometric and hydrodynamic nonlinearity, is established. A van der Pol wake oscillator is utilized to characterize the fluctuating lift forces. The finite element method is chosen to solve the coupled nonlinear fluid–structure interaction equations. The natural frequencies of the flexible riser are calculated to validate the method through comparisons with results from the literature. The modal analyses show that geometric nonlinearity has a significant effect on the natural frequency, and the critical internal velocity is reduced than those in linear analyses. The impacts of the gas volume fraction as functions of cross-flow velocity on the synchronization region, the displacement amplitudes, and the maximum stresses and frequency spectra have been investigated. The results show that an increase in the gas fraction results in the linear increase in natural frequencies and a wider synchronization region, and an increase in liquid flow rate led to the slight decrease in displacement amplitude and maximum stress within a small flow range.