With increasing environmental application of nanoparticulate zero-valent iron (nZVI), it is essential to explore the interaction of nZVI with dissolved organic matter (DOM) and clay mineral particles (CMPs) and its potential effect on the formation of DOM-mineral complex that may impact the carbon sequestration. The aggregation and adsorption behaviors of nZVIs (two bare nZVIs of different sizes and one carboxymethyl cellulose coated nZVI (CMC-nZVI)) and CMPs (kaolinite and montmorillonite) coexisting in DOM (humic acid and fulvic acid) solutions were systematically investigated. The bare nZVIs more easily formed heteroaggregates with montmorillonite than kaolinite in DOM solutions, while the CMC-nZVI tended to attach on kaolinite surface. The heteroaggregation and competition between nZVIs and CMPs could change their interfacial interaction with DOM and the ultimate immobilization of DOM was determined by the formed nZVI-CMP complexes, irrelevant to the addition sequence of nZVIs and CMPs. Compared with the individual CMPs alone, the formed bare-nZVIs-CMP heteroaggregates promoted the sequestration of DOM especially its aromatic carbon fractions, while the CMC-nZVI had no such effect. These findings will be helpful for the understanding of nZVI interaction with DOM and CMPs and the effect on the immobilization of organic carbon in the environment.