Graphene-related research has intensified rapidly in a wide range of disciplines, but few studies have examined ecosystem risks, particularly phytotoxicity. This study revealed that graphene significantly inhibits the number of wheat roots and the biosynthesis of chlorophyll, and altered the morphology of shoots. Humic acid (HA), a ubiquitous form of natural organic matter, significantly (P < 0.05) relieved this phytotoxicity and recovered the sharp morphology of shoot tips. Both graphene and graphene-HA were transferred from wheat roots to shoots and were found in the cytoplasms and chloroplasts. HA increased the disordered structure and surface negative charges, and reduced the aggregation of graphene. HA enhanced the storage of graphene in vacuoles, potentially indicating an effective detoxification path. The content of cadaverine, alkane, glyconic acid, and aconitic acid was up-regulated by graphene, greatly contributing to the observed phytotoxicity. Conversely, inositol, phenylalanine, phthalic acid, and octadecanoic acid were up-regulated by graphene-HA. The metabolic pathway analysis revealed that the direction of metabolic fluxes governed nanotoxicity. This work presents the innovative concept that HA acts as a natural antidote of graphene by regulating its translocation and metabolic fluxes in vivo. This knowledge is critical for avoiding the overestimation of nanomaterial risks and can be used to control nanomaterial contamination.