PurposeThe purpose of this paper is to develop a novel integrated risk assessment method from the system perspective to evaluate the risk of the cross-regional mega construction project (CMCP). Furthermore, this paper aims to confirm the core risk source factors and refine the risk management strategies of CMCPs through a case study.Design/methodology/approachBased on the analysis of the risk system of CMCPs, the concept model and risk assessment principles of integrated risk assessment were confirmed. The risk source factors and project objectives of the CMCP were identified from a literature review, export interview and case analysis. According to the vulnerability theory, the integrated risk assessment model was developed by involving vulnerabilities, threats, objectives and interaction of those factors synthetically. Then, ZW high-speed railway from China was analyzed to verify the feasibility and effectiveness of the proposed method.FindingsAs a result, 12 threat factors and 12 vulnerability factors were identified. Based on the case study, the main external threat comes from T13 (conflicts of interest between local governments) and T23 (harsh natural environment); the most easily exploited internal vulnerabilities were V11 (complexity of technology), V13 (lack of experience in technical application), V21 (inadequate experience) and V23 (lack of interest coordination mechanism). Moreover, the economic objective was most affected.Practical implicationsIt is essential to develop an interest coordination mechanism for CMCPs. The harsh natural environment is a critical factor, but it also promotes technological innovation and iteration. Public opinions in different regions are critical for CMCPs, and more emphasis should be placed on public opinion surveys of CMCPs. Moreover, diverse and flexible environmental protection strategies should apply in CMCPs.Originality/valueThis research has the following three contributions. First, based on vulnerability theory, an integrated risk assessment approach of CMCPs is developed, which enriches the risk measurement method system and provides inspiration for future research on risk in the construction industry. Second, the risk sources of CMCPs are identified from the perspective of vulnerability and threat to provide clear guidance for the risk management of CMCPs. Third, the core risk source factors and management strategies confirmed by the case study will be beneficial for various governments in different regions and project managers to optimize the project management scheme, as they are transferable management experiences.