Abstract: The emergent collaborative ecological agricultural models have thrived across the globe in recent years, displaying 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 significant accumulation of heavy metals within these agricultural systems. These heavy metals, magnified through the food chain, could pose serious health threats to humans. This study, through a systematic review of the variations in the physicochemical and biological properties such as organic matter content, pH levels, redox potential (E_h), 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. Particularly, the research attempts to establish a correlation between these differences and the speciation and bioavailability of heavy metals, aiming to provide a scientific basis for heavy metal risk management in ecological agriculture. The results indicate that the co-cultivation model fosters a series of environmental conditions conducive to mitigating the risk of heavy metals. Firstly, feed, duck manure, and shrimp shells significantly increase the organic content in the environmental media of the co-cultivation system, transforming free-state heavy metals into bound forms through adsorption and complexation. Additionally, duck urine, shrimp shells, and the application of lime can elevate the medium’s pH value, promoting the formation of insoluble precipitates with alkaline earth metals. Moreover, field activities involving ducks enhance the soil’s E_h value, improving the adsorption and precipitation of soluble heavy metals by iron and manganese oxides. 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. Such improvement in soil structure impedes 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 they secrete, can decrease the bioavailability of heavy metals, further mitigating the threat to the environment and health. Based on these analyses, this paper also proposes strategies for reducing the input of heavy metals, substituting chemical fertilizers and feed, thus controlling pollution at its source, which provides scientific guidance for agronomic management, heavy metal monitoring, and food safety assurance in co-cultivation agricultural models. Future research is necessary to further study and optimize these agricultural modules, promoting the healthy development of collaborative ecological agriculture globally.