There is a serious cognitive bias in the Three Modernizations of Railway (TMR), which restricts the transformation of digital and intelligent railway (DIR). The purpose was to form a methodology and theoretical support system suitable for the development of TMR through an all-round study of five dimensions (relationship model, evolution path, technical system, semantic modeling and capability evaluation), so as to unify understanding and provide ideas and methods for the overall improvement of the rapid iteration and innovation capability of DIR. Based on multiple perspectives, the TMR relationship model based on core values, typical characteristics and evolution process was constructed for the first time. Analyzed the architecture evolution path from single vertical application, distributed service, “cloud platform+service” V1.0, to “cloud native+ microservice” V2.0, an autonomous and controllable “Cloud-Edge-Terminal” collaboration. A new fusion technology system of business, system and application (BSA) based on CPS complex theory system was proposed. The tree like growth modeling based on the bionic function semantically expressed the evolution mechanism, and evaluated the ability through the entropy weight method. It can provide guidance for the optimal matching of digital intelligence transformation and enterprise strategic reconstruction, the best choice of evolution route, and the positive top-level design of full link transformation strategy. The research results show that railway informatization runs through the whole life cycle of railway development. Intelligence is the advanced stage of information and digitization. The three transformations are not the relationship of substitution and progression, but the mutually supporting coexistence and iteration relationship, with ontological development levels and characteristics differences. The research results can provide solutions for the differential development of coexistence, progression and iteration of three transformations. To provide systematic theoretical guidance and technical support for promoting the railway’s cloud based intelligence action and the transformation of digital intelligence. © 2023, Central South University Press. All rights reserved.