During urban flood events, the effect of urban rainwater pipeline siltation on overflow and stagflation intensifies the severity of flood disaster. However, the dynamic coupling mechanism of pipeline sedimentation and water flow is still unclear. To investigate the influence of two-phase flow on the hydraulic transport of siltation particles in rainwater pipelines, the numerical simulation model based on computational fluid dynamics (CFD) and discrete element method (DEM) is constructed. Then, the transient continuity governing equation and conservation equation of momentum are formulated to provide dynamic guidance and boundary constraint for CFD-DEM simulation. On this basis, the optimal drag force model and measurement method of equivalent siltation degree of pipeline are proposed and nested with CFD-DEM, and then, a high resolution numerical simulation model of pipeline sedimentation is formulated. The results show that the siltation degree affects the efficiency of drainage pipeline to a degree of 47%, which is much greater than the degree of influence of 33% for siltation length and 18% for slope. When the siltation degree is 0.1, the thickness of the silted bed surface under the influence of water flow scour is reduced by 33%. It revealed that the influence degree of siltation degree and flow rate was 168% and 20%, respectively, which was much larger than that of siltation length and slope. This study can provide technical support for subsequent pipeline cleaning and maintenance as well as flood prevention and mitigation.