Scientific collaboration has become an important part of the people-to-people exchanges in the Belt and Road Initiative, and remarkable progress has been made since 2013. Taking the 65 countries in the Belt and Road regions, hereafter called the BRI countries, as the research areas and using the collaborated WOS core collection papers to construct the inter-national scientific collaboration matrix, the paper explores the multiple structure and formation mechanisms of the scientific collaboration network of BRI countries through the GIS spatial analysis, social network analysis and negative binomial regression. The results show that: (1) at the global scale, knowledge flow is becoming more and more frequent, and the degree of internal collaboration within BRI countries is not as close as that of collaboration with other countries in the world. All the sub-regions of BRI regions have the most external collaboration links with Europe outside BRI regions. The global scientific collaboration network based on the BRI countries has changed from a "tripod" framework of Europe, USA, China to the "polygon" framework of Europe, USA, China, Japan, Canada, Australia and other dense regions. (2) The spatial structure of the collaboration network within the BRI countries is transformed from the "dual-core" type (China and Central & Eastern Europe) to the "multipole" type (Central & Eastern Europe, Russia, China, Singapore, India, Saudi Arabia, etc.). The hierarchical structure presents a typical "core-periphery" pattern, the core countries of which change from single core (China) to dual cores (China and India). In terms of control structure, the type has changed from one superpower (China) to multi great powers including China, India, Russia, Poland, Czech, Turkey, Malaysia and Iran, which presents a pattern of "high in the surroundings while low in the middle". (3) The main formation mechanisms of scientific collaboration network of BRI countries depend on scientific research ability, the level of economic development, the level of foreign linkage, and proximities such as geographical proximity, social proximity and language proximity. Among them, scientific research ability and social proximity play the most important role, while geographical distance gradually weakens the hindrance to scientific collaboration.