A railway alignment consists of a horizontal alignment and a vertical alignment. There is a strong coupling relation between the geographic environment, the horizontal alignment, and the vertical alignment if the terrain fluctuation is large or the horizontal features are complex. This chapter proposes a bi-level optimization model for railway alignment considering investment descent. The upper level is responsible for the horizontal alignment optimization, and the lower level is responsible for the vertical alignment optimization. A multi-stage optimization strategy including corridor scheme generation, initial scheme generation, and optimal scheme generation is suggested which not only upgrades the optimization efficiency but also confirms the suitable number of HPI and VPI gradually.