Under the new era’s context，a profound analysis of the spatiotemporal dynamics of the eco-innovation level of China’s marine economy holds significant theoretical and practical implications for advancing the construction of marine ecological civilization，propelling the high-quality development of the marine economy，and achieving the maritime power strategy. Since 2023，through the double-wheel drive of growth and innovation，green development and ecological protection，and digital empowerment and industrial upgrading，China has achieved remarkable results in the eco-innovative development of its marine economy，and at the same time，it is also facing opportunities and challenges in the political，economic，social and technological aspects. By constructing a three-stage theoretical model and evaluation index system，the spatio-temporal dynamics of China’s marine economic eco-innovation level from 2006 to 2021 is analyzed based on the diagnosis of the main influencing factors of China’s marine economic eco-innovation development. The results show that the average level of marine economic eco-innovation in the study period shows a steady upward trend，but there are more significant regional differences，and the differences show a tendency to become more and more intense. Finally，the Autoregressive Integrated Moving Average Model is used to predict the trend of eco-innovation development of China’s marine economy，and suggestions for policy responses to enhance the capacity and level of eco-innovation development of China’s marine economy are put forward.