Research on the sustainable development of the marine economy has conventionally revolved around the relationship between efficiency and development. However, most studies have neglected examining how excessive marine resource inputs under certain conditions may lead to resource congestion that restricts output efficiency and sustainable development. To fill this research gap, we optimized an index system to evaluate the input level of marine resources. Using the data of 11 coastal provinces and cities in China from 2000 to 2016, we calculated the congestion of marine resources and analyzed its spatiotemporal evolution and primary influencing factors. Finally, we separated the inefficiency driven by congestion from pure technical inefficiency. The results showed the following: (1) Grave, long-term marine resource congestion does exist in China, and it has evolved from fast to slow, strong to weak, and agglomeration to dispersion; (2) Congestion in the coastal areas has gradually weakened from north to south, and the center of gravity has experienced a shift from the center of China toward the north; (3) Marine resource congestion is mainly affected by the input of resource and capital, resource endowment, and industrial structure; (4) Factors leading to inefficiencies include resource congestion and long-term pure technical inefficiency. By combining congestion and efficiency, we produce values for studying inefficiency and the sustainable development of the marine economy, with the benefit of providing targeted strategies.