In response to the need for integrated bay planning and the high-quality development of bay area economies, this study examines the spatiotemporal evolution of marine enterprises and industrial synergy of marine new quality productive forces under blue acceleration. Focusing on six coastal cities in Fujian Province, China, we use enterprise registration data from 1998 to 2023 to analyze the scale, sectoral structure, and spatiotemporal evolution of marine enterprises, identify agglomeration cores and industrial synergy among marine new quality productive forces (NQPF) enterprises, and combine enterprise locations with land surface temperature data to examine changes in heatwave exposure among marine enterprises. After 2013, marine enterprises in Fujian expanded rapidly, shifting from a scattered distribution to concentration along a coastal belt, while the sectoral structure expanded beyond traditional marine industries toward activities centered on technology and services. Alongside blue acceleration, heatwave exposure among marine enterprises continued to intensify. In 2023, Fujian had 906 marine NQPF enterprises and 29 agglomeration cores. The mean DBCLQ between industries reached 0.45, indicating an industrial synergy network with multiple nodes and extensive linkages. Therefore, spatial optimization of marine industries, coordination across regions, and climate adaptation should be incorporated into future pathways for the sustainable development of marine economies in coastal cities.