Based on experiment data of the Sino-German comprehensive investigations in the Bohai Sea in 1998 and 1999, a simple coupled pelagic-benthic ecosystem multi-box model is used to simulate the ecosystem seasonal variation. The pelagic sub-model consists of seven state variables: phytoplankton, zooplankton, TIN, TIP, DOC, POC and dissolved oxygen (DO). The benthic sub-model includes macro-benthos, meiobenthos, bacteria, detritus, TIN and TIP in the sediment. Besides the effects of solar radiation, water temperature and the nutrient from sea bottom exudation, land-based inputs are considered. The impact of the advection terms between the boxes is also considered. Meanwhile, the effects of the microbial-loop are introduced with a simple parameterization. The seasonal variations and the horizontal distributions of the ecosystem state variables of the Bohai Sea are simulated. Compared with the observations, the results of the multi-box model are reasonable. The modeled results show that about 13% of the photosynthesis primary production goes to the main food loop, 20% transfers to the benthic domain, 44% is consumed by the respiration of phytoplankton, and the rest goes to DOC. Model results also show the importance of the microbial food loop in the ecosystem of the Bohai Sea, and its contribution to the annual zooplankton production can be 60%-64%. Based on experiment data of the Sino-German comprehensive investigations in the Bohai Sea in 1998 and 1999, a simple coupled pelagic-benthic ecosystem multi-box model is used to simulate the ecosystem seasonal variation. The pelagic sub-model consists of seven state variables : the phytoplankton, zooplankton, TIN, TIP, DOC, POC and dissolved oxygen (DO). The benthic sub-model includes macro-benthos, meiobenthos, bacteria, detritus, TIN and TIP in the sediment. Besides the effects of solar radiation, water temperature and the nutrient from sea bottom exudation, land-based inputs are also considered. The impact of the adversity terms between the boxes is also considered. Compared with the observations, the results of the multi-box model are reasonable. The modeled results show that about 13% of the photosynthesis primary production goes to the main food loop, 20% transfers to the benthic domain, 44% is consumed by the respiration of phytoplankton, and the rest goes to DOC. Model results also show the importance of the microbial food loop in the ecosystem of the Bohai Sea, and its contribution to the annual zooplankton production can be 60% -64%.