Sub-regional milling has become an important machining method in the production of free-form surface parts. However, due to complex tool paths, irregular surface topography can occur at the region boundaries, which in turn affects the performance of the part such as the light transmission, optical distortion and mechanical strength of non-metallic transparent material etc. It is vital for manufacturers and researchers to study the forming mechanism of topography at boundaries and then to control it to get the high quality of the machined surface. Therefore, this paper thoroughly investigates the formation of surface topography at the boundary of sub-regions in the five-axis machining process. First, the boundaries of sub-regions are classified. Simultaneously, swept surfaces of the cutting edge, taking into account the process parameters and tool path, are constructed. Then, the surface topography is calculated using an improved model based on dimension reduction theory. Furthermore, through simulation and experiments, the predicted surface topographies agree well with the measured ones. Finally, some conclusions are listed and the method in this paper can provide a reliable basis for manufacturing high-quality parts.