The paper calculates the economic system coupling coordination level of the countries along the Belt and Road Initiative (BRI) from 2000 to 2020. On this basis, the paper analyzes the eco-economic effects and mechanisms of the BRI using the difference-in-difference method. The research shows that the “Belt and Road” initiative will significantly improve the eco-economic system coupling coordination level of participating countries. A series of robustness tests, including parallel trend test, placebo test, control of other policy impacts, and replacement of the “Belt and Road” occurrence time, all show that this promoting effect exists. Second, the “Belt and Road” initiative has improved the coupling coordination level of eco-economic systems through trade and investment behavior, but its driving role still needs to be strengthened. The study confirms the global value of the BRI and offers a reference for crafting appropriate policies to enhance the sustainable development level of countries in the BRI.