In order to obtain the optimal geometric structure for sand transport in desert roads, this study fully utilizes the natural sand transport capacity of the desert roads, aiming to reduce occurrences of road damage due to sand burial. The research integrates Computational Fluid Dynamics (CFD) with optimization analysis theory. Various typical geometric structures of desert highway roadbed were modeled using the Design Exploration module in CFD. Optimization analysis methods were employed to model and compute the sediment transport optimization design on both the roadbed and road surface. Then, the initial sample points are obtained by using the Design of Experiments (DOE), and the response surface is established by using the Kriging model to obtain the change trend of the input parameters and the objective function. Finally, the cross-section parameters of the sediment transport subgrade corresponding to different inflow conditions are obtained. The results show that the sediment transport performance of embankment, cutting and semi-filled uphill subgrade is negatively correlated with the height of subgrade. The relationship between slope gradient and sediment transport performance of subgrade depends on the height of subgrade and the type of subgrade section. For embankment and cutting, when the subgrade height is less than 0.5 m, the sediment transport performance of the subgrade is positively correlated with the subgrade slope; however, when the subgrade height exceeds 0.5 m, the sediment transport performance is negatively correlated with the subgrade slope. For the semi-filled uphill flow subgrade, the sediment transport performance of the subgrade is negatively correlated with the subgrade slope. Comprehensive analysis shows that semi-filled and excavated downhill subgrade has the best sand transport performance, embankment subgrade has the second highest sand transport capacity, then cutting subgrades, while semi-filled and excavated uphill subgrade has the worst sand transport performance. The research conclusions provide valuable scientific guidance for the design of sand control embankment structures tailored to local conditions for desert highways. This is of significant importance for enhancing the sediment transport capacity of desert highways and prolonging their service life.