As a vital element affecting economic efficiency, the impact of marine industrial structure upgrading on marine economy has become a hot topic, and China is not an exception. This paper analyzed the dynamic relationship of marine industrial structure upgrading and marine economy efficiency to verity the “structural bonus” and “cost disease” effects. The results confirmed the existence of cost disease in China’s marine economy, although occasionally it illustrated structural bonus effects with the improvement of the regional marine economy efficiency. The spatial Durbin model (SDM) was introduced to study the spillover effect of local marine industrial structure upgrading (MISU) on the adjacent regions’ marine economy efficiency, and this spillover effect was verified to have agglomerate characteristics in China’s coastal areas. Then several countermeasures were proposed to realize marine ecological civilization and promote regional cooperation in the development of China’s marine economy.