The Belt and Road Initiative, proposed by the Chinese government in 2013, has exerted great influence, not only on geopolitics and the economy but also on scientific research. This paper investigates the relationship between scientific collaboration and knowledge production of the countries participating in the Belt and Road Initiative project. To this end, we used 314,678 co-authored papers and 6,226,577 paper publications in these countries from 2009 to 2018 to measure scientific collaboration and knowledge production, respectively. Additionally, we selected the country’s economic level, the number of specialized disciplines, and political stability as influencing indicators. Methodologically, we established a dynamic panel model and used the generalised method of moments to empirically analyze the relationship between the two and the influencing factors. The results reveal that the scientific collaboration and knowledge production of the countries along the Belt and Road Initiative are mutually reinforcing and show accumulative effects. The number of specialized disciplines and political stability are major influencing factors for scientific collaboration and knowledge production. Knowledge production can facilitate scientific collaboration by increasing number of specialized disciplines, economic development and political stability. Scientific collaboration can weaken the promotion of knowledge production in a similar way, exclusive of economic development.