The planning of railway logistics park is mostly upgraded from the existing railway freight facilities. Following the analysis of the main functions and the requirements of the railway logistics parks layout planning, an optimization functional areas layout model is proposed to minimize transshipment costs and maximize relevance, considering the constraints of existing railway freight facilities, functional area length, shape, direction requirements, and entrance and exit settings. Route-based distance is used in the model. Based on the NSGA-II algorithm, the continuous penalty factor is designed according to the satisfaction of the layout result to the constraint condition, and the constraint condition is converted into the objective function penalty value. On this basis, the slice tree coding sequence and multiple mutation methods are introduced, and the algorithm can effectively avoid falling into the local optimum. Case analysis demonstrates that the algorithm is effective and has high solution accuracy, and the layout scheme is reasonable.