For the layout of auxiliary stopping areas （ASAs） considering complex scenarios， taking the line with multi-target speed profiles as research objects， aimed at minimizing the number of ASAs and the train tracking interval， a multi-objective optimization model constrained with the safe operation of trains is established. In addition， a fast and elitist non-dominated sorting generic algorithm （NSGA-II） is designed and discussed. Moreover， to make the algorithm has a better performance， a population initialization strategy considering the layout characteristics of ASAs is proposed. The simulation results verify the effectiveness of the model and the algorithm on solving the layout problem of ASAs in complex scenarios. This paper can provide a new idea for solving related problems.