The institutional innovation and Marine economic resilience in China's coastal areas from 2003 to 2020 was measured by using the “vertical and horizontal” hierarchy method and the core variable method, and the spillover effect of institutional innovation on Marine economic resilience was analyzed by using the spatial Durbin model. The results show that the resilience of Marine economy fluctuates, and the horizontal areas are evenly distributed in space. The overall trend of institutional innovation is increasing and there is significant spatial differentiation. Institutional innovation can enhance the resilience of the local Marine economy, but the positive spillover effect on the resilience of the Marine economy in neighboring areas can only be fully demonstrated at a high level of institutional innovation. In general, institutional innovation is conducive to improving the resilience of the Marine economy in China's coastal areas.