We adopted two-way coupling of discrete and finite elements to examine the non-spherical ballast flow characteristics in a slurry pipe system during a shield project. In the study, we considered the slurry rheological property and the flake shape of the ballast. A ballast size between 17 and 32 mm under different slurry flow rates and ballast volumetric concentration conditions was investigated for determining the law through which the mass flow rate, detained mass percentage, and ballast distribution state are influenced. The results indicate that increasing slurry flow rate and the ballast volumetric concentration increase the mass flow rate; the influence of the latter is stronger. Increases in both in the slurry flow rate and the ballast volumetric concentration can reduce the detained mass percentage in the slurry discharging pipeline, whereas increasing the ballast size has the opposite effect. The increase in both the slurry flow rate and the ballast size changes the ballast motion state. Experiments verified the numerical lifting model of the ballast in the vertical pipeline. The measurements of the actual pipeline wall thickness verified that the simulation results regarding the ballast distribution were accurate.