Background and aim <p>Copper (Cu) contamination greatly impacts soil health and ecological environment. However, the intracellular (subcellar level) and extracellular (rhizosphere microbiology level) mechanism by which Cu-resistant PGPR enhance Cu tolerance in <i>Themeda japonica</i> is still unclear.</p> Methods <p>In this study, we isolated the Cu-resistant PGPR <i>Bacillus thuringiensis</i> GZNUTJ21 from rhizosphere of <i>T</i>. <i>japonica</i> and explored the mechanism of GZNUTJ21 to enhance Cu tolerance of <i>T</i>. <i>japonica</i> at subcellular and rhizosphere microbiology levels.</p> Results <p>GZNUTJ21 significantly increased the fresh weight of leaves and roots by 33.92% and 45.60% under Cu stress, respectively. It enhanced <i>T. japonica</i> tolerance by decreasing total Cu concentration in the roots and leaves, increasing the percentage of Cu in cell wall of these tissues, and elevating the percentage of inactive Cu forms (NaCl-extractable, CH₃COOH-extractable, HCl-extractable) in roots. GZNUTJ21 helped <i>T. japonica</i> resistance to Cu stress by decreasing the total and available Cu concentration in the rhizosphere soil. Under Cu stress, it also improved rhizosphere soil nutrients and enriched the Cu-resistant fungal groups associated with saprotroph and symbiotroph functions, enhanced fungal taxa interactions, and increased the relative abundance of Cu-tolerant beneficial bacterial communities (Proteobacteria, Acidobacteriota, Chloroflexi, Methylomirabilota, Ascomycota, Mortierellomycota, Basidiomycota and Glomeromycota). Partial least squares path modeling (PLS-PM) demonstrated that GZNUTJ21 positively impacted rhizosphere soil Cu chemical speciation, enzyme activities and bacterial community under Cu stress.</p> Conclusions <p>GZNUTJ21 enhanced <i>T. japonica</i> Cu tolerance by regulating distribution and chemical forms of Cu in <i>T. japonica</i>, increasing the relative abundance of Cu-tolerant beneficial microbial communities.</p>