ABSTRACT The increasing diversity of transportation modes and the rapid expansion of transportation networks present significant challenges for modeling multi-layer comprehensive transportation networks. It is crucial to determine whether aggregating certain layers is a viable option for balancing complexity reduction and information preservation. This decision defines the layered structures and informs subsequent analyses of these networks. Two-dimensional factors, namely topological structures and transportation attributes, are considered to enhance understanding of the similarities among network layers. The relative entropy and the Gini index are employed as metrics to assess information gain or loss resulting from layer aggregation or segregation, guiding decisions on network reduction. Furthermore, an integrated similarity measure, based on the quantum Jensen-Shannon divergence and the Gower distance, is utilized to identify the optimal aggregation sequences. Two real-world transportation networks serve as case studies. Results demonstrate that these transportation networks are more effectively maintained with layer-separated structures, preserving maximum information.