As the development of marine ecosystem models, the number of biological parameters increases, which consequently causes determination of these parameters to become a bottleneck in ecosystem modeling. Intrinsic regional characteristics of the ecosystem require spatial variability of biological parameters. To explore spatial difference of key parameters and their sensitivity, a highly resolved physical-biological ecosystem model ROMS-CoSiNE of the Bohai Sea and Yellow Sea is established. Sensitivity analysis of thirteen biological parameters indicates that strong difference in sensitivity exist between the south center Yellow Sea, the Bohai Sea and it’s coastal areas as well. The most sensitive parameter in the Bohai Sea is the initial slope of P-I curve. The second and third are the half saturation constant for zooplankton grazing and the maximum specific growth rate of zooplankton. For the south Yellow Sea, the most sensitive parameters are the maximum specific growth rate of zooplankton, the death rate of phytoplankton and the initial slope of P-I curve. Based on sensitivity distribution and phytoplankton budget, it is concluded that the low transparency in the Bohai Sea and high transparency in the Yellow Sea are mainly responsible for spatial difference of sensitivity relative to the initial slope of P-I curve. Spatial difference of sensitivity relative to the maximum specific growth rate of zooplankton and the death rate of phytoplankton, is affected by phytoplankton amount difference between the Bohai Sea and the Yellow Sea, and related to high nonlinearity in the ecosystem.