Abstract: Surface roughness significantly affects the aerodynamic and thermal characteristics of high-speed vehicles, and reducing surface roughness is an effective approach for drag reduction and thermal protection. To maximize the drag and heat flux reduction benefits of smooth areas under the constraint of limited surface treatment area, the direct simulation Monte Carlo method was employed to simulate the transition flow regime for two typical geometries: a plate and a blunted cone with distributed smooth strips. The accommodation coefficient of the smooth surface was obtained via molecular dynamics simulations, while the completely diffuse reflection model was used to represent the conventional rough regions. In this manner, the surface characteristics corresponding to the lower and upper bounds of roughness were characterized, and spatially nonuniform accommodation-coefficient boundary conditions were established to investigate the mechanisms underlying the effects of the spatial distribution of surface roughness on the aerodynamic characteristics of the vehicle. The results show that smooth strips can induce the redevelopment of the boundary-layer flow over the vehicle surface, resulting in friction and heat-flux losses or abrupt changes in the transition regions between smooth and rough surfaces. For small regions, such as the vehicle nose and leading edge, where skin friction increases, multiple continuous or discrete smooth strips should be distributed in the central part of the local region to fully exploit the friction and heat-flux losses associated with the transition regions. For large regions, such as the vehicle body, where skin friction and heat flux decrease, the smooth strips should be arranged continuously in the downstream part of the local region when the local flow angle of attack is relatively large, thereby minimizing abrupt changes in friction and heat flux across the transition regions. Conversely, when the local flow angle of attack is relatively small, the smooth strips should be arranged continuously in the upstream part of the local region. At a strip coverage ratio of 50%, the continuous mid-region arrangement (D4) and the discrete interleaved arrangement (D7) on the flat plate exhibit comparable reductions of approximately 13%–15% in both skin friction and heat flux. For the blunted cone, the continuous rear-region arrangement (D5) yields the best performance, achieving a total drag reduction of about 12%. This study provides a theoretical basis and numerical reference for the spatial layout design of polished regions on high-speed vehicle surfaces.