Conventional studies usually assume that the train surface is smooth, so as to simplify the numerical calculation. In fact, the surface of the train is irregular, which will change the flow characteristics in the boundary layer and further affect the aerodynamic performance of a train. In this work, roughness is applied to the roof of a 1:25 scaled train model in the form of longitudinal strips. Firstly, the improved delayed detached eddy simulation (IDDES) method is adopted to simulate the aerodynamic performance of the train model with both smooth and rough surface, which are subjected to crosswind. Results show that the side force coefficient and the roll moment coefficient subjected to rough model decreased by 3.71% and 10.56% compared with the smooth model. Then, the width, height and length of the strips are selected as variables to design different numerical simulation schemes based on the orthogonal experimental design method. Through variance analysis, it can be found that four design parameters have no significant effect on the side force coefficient. Meanwhile, for the roll moment coefficient, the length of the strips in the straight region of the train has a significant effect and the width of the strips has a highly significant effect on it. These conclusions can provide a theoretical basis to improve the aerodynamic performance of the high-speed train subjected to crosswind.