China’s Belt and Road Initiative (BRI) is an unprecedented global development program that involves nearly half of the world’s countries [1]. It not only will have economic and political influences, but also may generate multiple environmental challenges and is a focus of considerable academic and public concerns [2, 3, 4, 5, 6]. The Chinese government expects BRI to be a sustainable development, paying equal attention to economic development and environmental conservation [7]. However, BRI’s high expenditure on infrastructure construction, by accelerating trade and transportation, is likely to promote alien species invasions [5], one of the primary anthropogenic threats to global biodiversity [8]. BRI countries may have different susceptibilities to invasive species due to different financial and response capacities [9]. Moreover, these countries overlap 27 of 35 recognized global biodiversity hotspots [10]. Identifying those areas with high-invasion risks, and species with high invasive potentials within BRI countries, is therefore of vital importance for the sustainable implementation of the BRI, and the development of early, economical, and effective biosecurity strategies [11]. In response, we present here a comprehensive study to evaluate invasion risks by alien vertebrates within BRI. We identified a total of 14 invasion hotspots, the majority of which fall along the six proposed BRI economic corridors, with the proportion of grid cells in invasion hotspots 1.6 times higher than other regions. Based on our results, we recommend the initiation of a project targeting early prevention, strict surveillance, rapid response, and effective control of alien species in BRI countries to ensure that this development is sustainable.