Under the operation of strong crosswinds, the aerodynamic performance of high-speed trains (HSTs) will be seriously deteriorated when the transition section of flat ground and semi-cutting and semi-embankment (FGSCSE) is traversed, and the setting of windbreaks will help to slow down the impact of strong crosswinds on the trains. In this study, a three-dimensional coupled computational fluid dynamics numerical model to assess the aerodynamic performance of train–windbreak–FGSCSE–air system is developed. A comparative assessment is carried out to identify the variations in aerodynamic performance on the train carriage: no windbreak (NW), 50% ventilation windbreak (VW), and solid windbreak (SW), and the reasons for these variations are elucidated by examining the flow field structure's evolution. Furthermore, the operational safety of the train is discussed based on the indicator of wheel unloading ratio (fΔQ). Across the three distinct conditions, significant abrupt changes in aerodynamic load coefficients (ALCs) and the shedding of vortex structures are experienced by HSTs traversing the FGSCSE transition sections. Compared to the VW condition, the NW and SW conditions result in a greater number of shedding vortices on the leeward side and the tail of the train, and the VW condition results in the smallest magnitude of ALCs fluctuation. The power spectral density peak values of the aerodynamic loads follow the order: SW > NW > VW. Upon the train fully enters the subsequent operational environment, the VW condition has the smallest standard deviation of these coefficients. The standard deviations of CFy, CFz, CMx, CMy, and CMz for the head train in the VW condition are only 57.17% (46.81%), 55.85% (54.15%), 72.74% (34.62%), 57.99% (51.92%), and 44.60% (43.82%) of the corresponding values in the NW (SW) condition, respectively. In the NW, VW, and SW conditions, the fΔQ exceeds 0.9 when the wind speeds reach 30, 40, and 35 m/s, respectively. The windbreak with a ventilation rate of 30% performs the best, providing the most effective safety and stability for train operation.