The structure of suspended particles and organic carbon storage in jellyfish-shellfish-fish-prawncultured ponds were investigated, with the goal of clarifying the characteristics of the ecological structure and function of polyculture ponds, as well as providing baseline data of the carbon cycle under different culture models to facilitate development of low-carbon fisheries. The experiments were carried out in two Rhopilema esculentum-Sinonovacula constricta-Paralichthys olivaceus-Fenneropenaeus chinensis polyculture ponds (latitude 39°51' N; longitude 124°09' E) in Donggang, Liaoning province from May to October 2013. The concentration of total suspended particles was (67.12±6.03) mg/L and (70.05±7.63) mg/L in the two experimental ponds. Of the total suspended particles, the percentage of inorganic suspended particles was 72.57% and 75.49%, and the percentage of organic suspended particles was 27.43% and 24.51% in the two ponds. The percentages of dry weight of bacteria and detritus, phytoplankton, and zooplankton of the total suspended particle matter were 27.15% and 24.20%, 0.15% and 0.22%, and 0.13% and 0.09%, respectively. The mean concentration of total organic carbon (TOC) was (7.31±1.51) mg/L and (6.42±1.31) mg/L in the two experimental ponds. Relative to TOC, the percentages of dissolved organic carbon was highest at 76.33% and 70.56%, followed by particles of organic carbon (23.67% and 29.44%), bacteria carbon (7.96% and 7.18%), detritus carbon (14.70% and 20.90%), phytoplankton carbon (0.56% and 0.95%), and zooplankton carbon (0.45% and 0.41%). The concentration of total suspended particles in the R. esculentum-S. constricta-P. olivaceus-F. chinensis polyculture ponds was high, and the inorganic suspended particles was the most important component of the total suspended particles in this ecosystem; bacteria and detritus were the main components of the organic particles. These results indicate that bacteria and detritus play a very important role in nutrient cycling and energy flow in this polyculture ecosystem.