Achieving marine sustainable development goals requires improving the quality of the marine economy. In this study, we constructed a multi-dimensional evaluation index system to quantify the high-quality development of the marine economy (HDME) and digital economy for China’s 11 coastal regions between 2012 and 2020, and systematically explored the mechanisms between the digital economy, marine industrial structure upgrading, and high-quality development of the marine economy. We further empirically analyzed the influence of the digital economy and marine industrial structure upgrading on the HDME by using the static and dynamic spatial Durbin model and threshold model. We found that the digital economy improved the HDME of local and neighboring regions, and the sub-dimensional indicators had a significant heterogeneous effect. The marine industrial structure upgrading only positively affected the quality of the marine economy in neighboring areas. Furthermore, the digital economy and marine industrial structure upgrading also had synergistic effects on improving the marine economy, which mainly depended on digital infrastructure and digital industrialization. There also existed digital infrastructure and digital industrialization thresholds within marine industrial structure upgrading, affecting the HDME. Our results provide new insights for the green and sustainable development of the marine industry and marine economy from a broader technical perspective in the digital age. Governments should recognize the spatial spillover and synergistic effects of the digital economy and marine industrial structure between different regions and implement policies considering their impacts to achieve the marine sustainable development goals.