• The framework is proposed using security-driven and safety-oriented methods. • SSCA is constructed through both top-down and bottom-up perspectives. • The regulatory development of SSCA is analysed among different transport modes. • It strikes new research directions for digitalised and autonomous transport vehicles. Transportation is sensitive to risk. Given the fast development of digitalisation and automation of transport systems in the past decade, new types of security risks (e.g. cyberattacks) emerge within the context of transport safety research. To enable the integrated analysis of emerging security and classical safety-related risks in a holistic manner, safety and security co-analysis (SSCA) is highly demanded for accident prevention. SSCA in transport systems will benefit the risk analysis of complex cyber physical transport systems facing challenges from both hazards and threats. However, the nature of hazard and threat-based risks is fundamentally different, which leads to the various difficulties of analysing them on the same plane. They include the use of different risk parameters, the uncertainty levels of the risk input and the methodologies of risk inference. To address such concerns, this study firstly reviews the literature on SSCA and compares the employed methodologies and their applications within the context of transport systems. Taking into account the advantages of both security-driven and safety-oriented methods, a conceptual framework is proposed to imply the insights on SSCA for transportation through both top-down and bottom-up perspectives, followed by a quantitative illustrative case study. Then, the regulatory development and evolution of SSCA in transport in practice is analysed across different transport modes, which configures initiatives’ interrelations for a cross-fertilisation purpose. As a result, the findings reveal new research directions for the safety of digitalised and/or autonomous transport vehicles and aid in the formation of future transport safety study agendas.