A dynamic model is proposed to describe an integrated multi-trophic aquaculture (IMTA) system, including nutrients, detritus, phytoplankton, zooplankton and scavenger. The dynamic properties of the model are fully studied. Ecological reproductive indexes for the survival of phytoplankton, zooplankton, and scavenger play crucial roles in the construction of IMTA structure. Parameter values of the model are estimated based on experimental data. The study reveals that zooplankton in integrated aquaculture systems exhibit a dualistic function, potentially either enhancing or suppressing the growth of scavengers. This finding provides a mechanistic explanation for the paradoxical phenomenon observed in some marine ranching, where integrated aquaculture fails to enhance productivity, thereby challenging the conventional assumption of its universally positive effects. Furthermore, the study identifies key traits of zooplankton that promote scavenger production. Through bifurcation analysis of resource inputs, the research delineates the mechanistic basis for optimizing scavengers yield while maintaining ecosystem stability. These insights provide a theoretical foundation for enhancing the structure and sustainability of multi-trophic aquaculture systems.