Intercity railway transit is the primary way to transfer passengers and freight over long distances on land. The design of an intercity railway alignment is usually challenging and complex because of great topographic variations and intersections with many existing geographic objects. This paper presents a bilevel optimization model for intercity railway alignment (BRAO) following the horizontal-vertical alignment design philosophy. The upper level is the horizontal alignment optimization, while the nested lower level is the vertical alignment optimization. A multistage augmented differential evolution algorithm is adopted for the solution at both levels. BRAO could generate corridor alignment, initial alignment, and optimal alignment through different allocations of the number and boundaries of decision variables. A real-world case study of railway design is conducted to verify the effectiveness of the BRAO model based on a geographic information system.