Abstract: In recent years, emergent collaborative ecological agricultural models have thrived worldwide, displaying a robust growth momentum. However, longstanding agricultural practices involving the excessive combined use of feed, chemical fertilizers, and pesticides, along with improper treatments such as irrigation with substandard wastewater, have led to the significant accumulation of heavy metals within these agricultural systems. These heavy metals, which are present throughout the food chain, pose serious health threats to humans. This study, through a systematic review of the variations in physicochemical and biological properties, such as organic matter content, pH levels, redox potential (Eh), and microbial activity, in different types of paddy-based co-cultivation systems, delves into the differences in heavy metal transformation and accumulation between monoculture systems and those integrating rice with ducks or shrimp. In particular, this study attempted to establish a correlation between these differences and the speciation and bioavailability of heavy metals, with the aim of providing a scientific basis for heavy metal risk management in ecological agriculture. These results indicate that the co-cultivation model fosters a series of environmental conditions that are conducive to mitigating the risk posed by heavy metals. 1) Feed, duck manure, and shrimp shells significantly increased the organic content in the environmental media of the co-cultivation system, transforming free-state heavy metals into bound forms through adsorption and complexation. 2) Additionally, duck urine, shrimp shells, and lime can increase the pH of the medium, promoting the formation of insoluble precipitates with alkaline earth metals. 3) Moreover, field activities involving ducks enhanced the soil’s E_h value, improving the adsorption and precipitation of soluble heavy metals by iron and manganese oxides. 4) Furthermore, the movement of ducks and shrimp not only ameliorates soil texture, but also reduces the mobility and bioavailability of heavy metals, thereby diminishing their transfer risk in the food chain. 5) Such improvements in soil structure impede the mobility of heavy metals and their uptake by plants, subsequently reducing their transmission risk through the food chain. Simultaneously, an increase in the abundance and diversity of microbial communities, along with the extracellular polymers that they secrete, can decrease the bioavailability of heavy metals, further mitigating environmental and health threats. Based on these analyses, this study also proposes strategies for reducing the input of heavy metals, substituting chemical fertilizers and feed, and thus controlling pollution at its source. This provides scientific guidance for agronomic management, heavy metal monitoring, and food safety assurance in co-cultivation agricultural models. Further research is necessary to study and optimize these agricultural modules to promote the healthy development of collaborative ecological agriculture globally.