To address the reduction in structural strength and the decreased safety of separated-type aqueduct bodies due to erosion damage caused by sediment-laden flow, an erosion damage model for the aqueduct structure was established based on the theory of water-sediment two-phase flow erosion damage. This model incorporates the RNG k-ε turbulence model and the Discrete Phase Model (DPM). The FLUENT software was employed to simulate and analyze the erosive damage effects of sediment-laden flow on the separated-type aqueduct under various operating conditions. Additionally, the influence of pier heads with different aspect ratios on the flow field at the aqueduct inlet and outlet was simulated. The results indicate that the unsteady flow characteristics at different locations of the aqueduct and the geometric discontinuities in the aqueduct structure are key factors influencing erosion damage. The erosion damage rate of the structure is positively correlated with flow discharge, sediment concentration, and particle size. Specifically, variations in the frequency and intensity of sediment particle impacts on the wall can exacerbate the erosion damage. The aspect ratio and shape of the separated-type pier heads at the aqueduct inlet and outlet significantly affect the flow pattern. Compared to the common semi-circular inlet and outlet piers, when the aspect ratio of the pier head is in the range of 1.5–2.0 and the shape is streamlined, it can effectively improve the flow pattern at the aqueduct inlet and outlet sections, mitigate the flow-blocking effect of vortices, and significantly reduce the erosion damage rate of the aqueduct. The research findings can provide a technical reference for the optimal design of separated-type aqueducts and the enhancement of their erosion resistance.