During flash flood events, a prominent size segregation phenomenon often occurs in the mixture of sediment particles of varying diameters moving with the floodwaters. However, the impact of the inherent inhomogeneity of the sediment on its transport process continues to be unclear. This study evaluates the sorting phenomenon in the transport behavior of flood-impacted, loosely deposited sediment particles originating from steep tributary feeders in mountain channels. To achieve this objective, a computational framework integrating Computational Fluid Dynamics and Discrete Element Method (CFD-DEM) was utilized to directly simulate the detailed paths of all particles. After validating the CFD-DEM model, we investigated the influence of the sediment particles’ coefficient of uniformity (Cu) on sediment transport characteristics. The results suggest that under different Cu values, coarse particles initially accelerate rapidly but later slow down and converge to a consistent speed, whereas fine particles demonstrate a more uniform speed increase and eventually maintain a constant velocity. With rising Cu, the peak degree of sorting between coarse and fine particles first increases and then stabilizes. The temporal variation of the dimensionless sediment transport rate of any sediment component at a given section can be represented using a modified dual-branch Weibull function. The overall transport process can be determined through linear superposition based on mass proportion. Additionally, we found that the heterogeneous characteristics of the sediment provide a mode of overall sediment transport where fine particles roll at the bottom, while coarse particles slide and saltate at the top, leading to reduced frictional dissipation in the movement of coarse particles. This phenomenon is commonly observed in mountain flood channels with slopes less than 60 degrees. These findings bolster the explanation for the poor application of existing sediment transport rate formulas in flash flood channels.