There is no clear protocol for quantitatively assessing connectivity impacts of mega transport infrastructure projects designed to reconfigure the transportation networks of entire regions and sub-continents. We developed a protocol that uses open-source data and tools to complete the analysis, starting from data acquisition, network preparation, to the analyses of centrality (accessibility) and percolation (agglomeration). We tested our protocol on the China-Pakistan Economic Corridor (CPEC), the flagship project of China’s Belt and Road Initiative. We found that the CPEC outcomes will be mixed, improving connectivity and economic growth for key cities but widening development inequality. The benefits of our protocol are threefold. First, it extends the existing literature by providing a quantitative method for estimating the importance of new transportation networks brought by BRI. Second, it can be replicated to different scales and locations with easy-access open data. Third, the processing platforms we use are all open source, making it accessible for local governments and analysts in resource scarcity typically found in BRI projects. The protocol can be adopted by the government, academic, funding, private, and community stakeholders to effectively assess BRI-related investments.