The metro system is the trunk of the transportation network in large cities. The most common construction method for metro projects is the shield method which makes the direct investment closely related to the length of horizontal alignment and the energy consumption of a train operation closely related to the slope composition of vertical alignment. This chapter introduces a double line optimization for the metro alignment in which both equality and inequality constraints are considered. To deal with the density obstacles in the geographical environment for horizontal alignment optimization, we propose three strategies, i.e. direct optimization, optimization with an existing seed, and optimization in successive two stages. Three practical cases are explained to verify the efficiency of the three strategies respectively. In the optimization of metro vertical alignment optimization, we analyze three operating modes i.e. coasting mode, cruising mode, and hybrid mode, and propose their corresponding optimization models. Afterward, the traction calculation of the metro train is explained in detail to realize the calculation of the objective functions. Nine cases are explained to verify the efficiency of the three optimization models of vertical alignment respectively.