Currently, accelerating the construction of a new development pattern with dual economic circulations is strategically significant for enhancing the autonomy and sustainability of China’s economic development. First of all, this paper, from the perspective of green innovation in marine science and technology, measures its efficiency using the SBM super-efficiency model. Then, a coupling coordination model calculates the coordination degree of dual economic circulations after measuring the domestic and international economic circulations based on the TOPSIS method. Secondly, a two-way fixed effects model is employed to examine the impact of green innovation in marine science and technology on domestic economic circulation, international economic circulation, and dual economic circulations. The study finds that green innovation in marine science and technology effectively promotes domestic economic circulation, international economic circulation, and the dual economic circulations. Additionally, green innovation in marine science and technology mitigates the impact of inter-regional resource misalignment on domestic economic circulation and influences international economic circulation by promoting the high-quality development of the marine economy. Finally, it is discovered that green innovation in marine science and technology exhibits a single-threshold heterogeneous effect on domestic economic circulation and international economic circulation.