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E-waste generation has become a major environmental issue worldwide. Heavy metals (HMs) in e-waste can be released during inappropriate recycling processes. While their pollution characteristics have been studied, the migration and transformation of different multi-metal fractions in soil–plant system of e-waste dismantling sites is still unclear. In this study, pot experiments were conducted to investigate the migration and transformation of different multi-metal fractions (Cu, Pb, Zn and Al) in the soil–plant system using two Chinese cabbage cultivars (heavy metals low-accumulated variety of Z1 and non-low-accumulated Z2) treated with or without biochar. The result showed that the acid-soluble fraction of Cu, Pb, Zn and Al in soil decreased by 5.5%, 55.7%, 7.8% and 21.3%, but the residual fraction (ResF) of them increased by 48.5%, 1.8%, 30.9% and 43.1%, respectively, when treated with biochar and plants, compared to that of the blank soil (CK). In addition, Pb mainly existed as a reducible fraction, whereas Cu existed as an oxidisable fraction. Biochar combined with plants significantly increased the ResF of multi-metals, which reduced the migration ability of Pb among all other metals. The relative amount of labelled 13C in the soil of Z1 was higher than that of Z2 (25.4 fold); among them, the Gram-negative bacteria (18-1ω9c, 18-1ω7c) and fungi (18-2ω6c) were significantly labelled in the Z1-treated soil, and have high correlation with HM migration and transformation. In addition, Gemmatimonadete were significantly positive in the acid-soluble fraction of HMs, whereas Ascomycota mostly contributed to the immobilisation of HMs. Therefore, the distribution of fractions rather than the heavy metal type plays an important role in the HM migration in the soil–plant system of e-waste dismantling sites.