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Abstract Particulate organic matter (POM) acts as a metals sink in soil, but only a few studies focused on the interaction of POM and heavy metals in paddy soil. The aim of this study is to investigate the interaction between POM and Copper (Cu)/Zinc (Zn). Two levels of Cu (100, 400 mg kg−1) and Zn (250, 500 mg kg−1) were used in a soil culture experiment. Our results showed that POM was porous structure and varied in size. Hydroxyl and carboxyl involved in POM adsorption of Cu and Zn. Rhizosphere effects roughen the surface of POM and enhanced the capacity of POM on heavy metals absorption. Cu-humic (26.2–33.9%) and Cu-citrate (38.5–42.4%) were dominated in POM, and Cu-goethite (41.7–57.7%), Cu-sulphide (6.6–27.6%) was dominated in soil. Rhizosphere effects decreased the proportion of organic-bond Cu along with the increasing the proportion of Cu-sulphide in POM. Addition of Cu and Zn inhibited the degradation of POM but rhizosphere effects promoted. Carbon content was increased in POM by heavy metal and rhizosphere effects. Our findings indicated that POM tended to retain the heavy metals in soil and heavy metals inhibited the degradation of POM, however, rhizosphere effects decreased the stability of POM-metals interactions. Graphical abstract Image 1 Highlights • Hydroxyl and carboxyl were involved in POM adsorption of heavy metals. • Cu was mostly bonded to organic acids in POM, whereas most of Cu was combined with goethite and S in soil. • Rhizosphere effects decreased contents of Cu-organic acids and increased contents of Cu 2 S in POM. • Cu and Zn inhibited the degradation of POM but rhizosphere effects stimulated. • Heavy metals and rhizosphere effects changed the components of POM. [ABSTRACT FROM AUTHOR]