This paper presents a novel approach to optimizing movement in urban areas through a dynamic multi-layer walkability model. This research uncovers new facets of walkability modeling within transit-oriented movement, aligning pedestrian pathways (Routes) with urban architecture, public spaces, and green spaces (Nodes). The dynamic multi-layer (DML) approach involves optimizing both the Nodes and Routes of the transit system using a multi-objective optimization method. This method improves accessibility and connectivity by aggregating the results of agent-based modeling for route simulations and considers multiple criteria, including greenness, distance to transit, and destination accessibility. Experimentation with a case study produced several findings that underscore the value of multi-layered models for transit movement and the power of computational methods in optimizing both Nodes and Routes. This discovery offers valuable insights into the DML process and its potential applications in the field of urban design and architecture.