Viologens, especially paraquat (PQ) and its analogs, were commonly used as herbicides. However, their high toxicity poses considerable risks to human life and the environment. In this paper, we report an effective strategy for the encapsulation of toxic herbicides by a heteromolecular aggregate (HA) and could be used for the treatment of viologen poisoning. This new protocol is based on host−guest chemistry and involves the collaborative encapsulation of viologens, which led to instantaneous precipitation with single viologens and their trapped toxic species. ITC, solution-state and solid-state NMR, fluorescence, and single crystal X-ray crystallography studies indicated that the HA could form highly stable complexes with all three viologens. Electrochemical experiments showed that the encapsulation could significantly reduce the redox potentials of viologens (no visible peaks). Proton NMR analyses showed that the performance well exceeded the previous reports, achieving efficient viologen removal. Further studies in cells and zebrafish showed that encapsulation by HA could significantly increase cell viability and decrease the mortality rate of zebrafish. As a result, HA might have great potential application in the clinical treatment of viologens poisoning. To our knowledge, this is the first report of HA for the collaborative encapsulation and complete removal of PQ and its analogs at wide concentration ranges.