To reveal the material flow characteristics of mariculture pond ecosystems of shellfish monoculture and shellfish-shrimp integrated culture, two Ecopath models composed of 14 and 15 functional groups respectively were constructed. The results showed that the material transfer efficiency between Ⅰ and Ⅱ trophic levels of the integrated culture mode (52.1%) was higher than shellfish monoculture mode (26.5%), and the proportion of material flows in the detritus group (20.81%) was also higher than the shellfish monoculture mode (4.64%). Compared to the shellfish monoculture mode, the key species of the integrated culture mode changed from macroplankton to Litopenaeus vannamei, while the mixed trophic impact analysis showed that the shrimp group obviously affected plankton and detritus groups, resulting in the fact that effective efficiency (EE value) of zooplankton increased, and the phytoplankton EE value decreased. The mixed trophic impact of shellfish group was not changed between the two modes. The Finn's cycling index of the monoculture and integrated culture system were 2.75% and 13.21%, the connectance index were 0.256 and 0.250, and the system omnivory index were 0.049 and 0.065, respectively. The results suggest that the food web in integrated culture mode was more complex, and the system structure was better than that of the shellfish monoculture mode, indicating that there is improvement potential for the two system. In order to improve the system stability, feed utilization and breeding efficiency stability, functional groups at different trophic levels could be introduced to the system.