Hydrocarbon flows in a marine riser may appear in multiple phases with varying flow patterns, among which, slug flows are known to exhibit complex flow characteristics due to fluctuations in multiphase mass, velocities, and pressure changes. Bulk of the literature concerning internal single and two-phase flow induced vibrations have largely focused on the use of a linearized tension beam model. In this study, the fluid-structure interaction phenomena of a submerged long flexible cylinder conveying two-phase slug flows is investigated taking into account the geometric and hydrodynamic nonlinearities. A semi-empirical theoretical model which consists of nonlinear structural equations of coupled out-of-plane, in-plane and axial structural motions is presented for the analysis and prediction of two-phase slug flow induced vibrations (SIV). The model includes equations involving centrifugal and Coriolis forces to capture mass variations in the slug flow regime. A numerical space-time finite difference approach combined with a frequency domain analysis is used for analyzing the highly nonlinear three-dimensional responses. The model assumes constant geometric properties across the span of the cylinder and utilizes an idealized slug unit concept, wherein slug properties are considered to be fully developed and undisturbed by pipe oscillations. Model validations are performed through comparisons with published experimental internal flow-induced vibration results. Parametric study captures the effects of several key slug characteristics on the vibration responses of a fluid-conveying cylinder. The results demonstrate amplitude-modulation response, mean displacements, three-dimensional cylinder displacements due to geometric nonlinear couplings and the influence of internal flow velocities. Higher dominant modes and oscillation frequencies were observed when the cylinder experiences large amplitude motions at specific slug formations. A new dimensionless parameter is introduced to predict scenarios of high amplitude oscillations for long flexible cylinders carrying two-phase slug flows.