Abstract: Bay is a relatively independent and complete ecosystem with superior location and resource advantages.It faces huge utilization demands, which increase the environment pressure.Ecosystem based management (EBM) is the mainstream paradigm of resource and environment management in international, providing new theoretical for solving ecological and environmental crisis.This paper analyzed the characteristics of bay ecosystem and ecological environment problems, put forward ecosystem-based integrated management framework of bay(BEBM), including principles, goals, and specific control strategies based on the theory and practices of EBM.Control strategies included five aspects:develop integrated space planning of watershed-bay, control land-based pollution by changing land use of the watershed, maintain hydrodynamic conditions and protect key habitat, establish integrated watershed-bay management mechanism.It will provide references for bay development and protection.