A custom-built large-scale flume was utilized to conduct heterogeneous aggregation experiments between microplastics and sediment under the influence of shear flow, and thus to analyze their morphological characteristics and aggregation mechanisms. Two typical types of microplastics (PMMA and PS) in the upper Yangtze River were selected for our investigation. The sediment sample configuration was determined based on the mineral composition and the grading of the suspended sediment in the Three Gorges Reservoir backwater area. The results showed that under turbulent shear flow, the particle size of flocs formed by the heterogeneous aggregation of microplastics and sediment was larger than that of flocs formed by homogeneous sediment aggregation. The number of microplastics adsorbed on microplastic-sediment flocs per milliliter of sample increased rapidly with the increase in shear rate of the water flow. The results of scanning electron microscopy and energy dispersive spectroscopy analyses showed that heterogeneous aggregation of sediment with the PMMA and PS occurred under hydrodynamic conditions. During aggregation, electron transfer and shifts in chemical states occurred, leading to the formation of unsaturated bonds (C C). The variation in the binding energy of PMMA functional groups was greater than that of PS. This suggests that PMMA lost more electrons in this process, resulting in a higher surface charge and propensity increase to aggregate with sediment.