Arbuscular mycorrhizal fungi (AMF) can alleviate heavy metal phytotoxicity and promote plant growth, while the underlying mechanisms of AMF symbiosis with host plants under manganese (Mn) stress remain elusive. A pot experiment was carried out to investigate the plant growth, micro-structure, Mn accumulation, subcellular distribution, chemical forms, and physiological and biochemical response of Rhus chinensis inoculated with Funneliformis mosseae (FM) under different Mn treatments. The results showed that compared with plants without FM, FM-associated plants exhibited higher growth status, photosynthetic pigments, and photosynthesis under Mn stress. FM-associated plants were able to maintain greater integrity in mesophyll structure, higher thickness of leaf, upper epidermis, and lower epidermis under Mn treatment, and promote leaf growth. Mn accumulation in leaves (258.67–2230.50 mg kg−1), stems (132.67–1160.00 mg kg−1), and roots (360.92–2446.04 mg kg−1) of the seedlings inoculated with FM was higher than non-inoculated ones. FM-associated plants exhibited higher osmotic regulating substances and antioxidant enzymes’ activities under Mn exposure, suggesting lower Mn toxicity in FM inoculated seedlings, despite the augment in Mn accumulation. After FM inoculation, Mn concentration (151.04–1211.32 mg kg−1) and percentage (64.41–78.55%) enhanced in the cell wall, whilst the transport of Mn to aerial plant organs decreased. Furthermore, FM symbiosis favored the conversion of Mn from high toxic forms (2.17–15.68% in FEthanol, 11.37–24.52% in Fdeionized water) to inactive forms (28.30–38.15% in FNaCl, 18.07–28.59% in FHAc, 4.41–17.99% in FHCl) with low phytotoxicity. Our study offers a theoretical basis for remediation of the FM- R. chinensis symbiotic system in Mn-contaminated environments. Display omitted •Mn stress led to an obvious decrease in plant growth and oxidative damage in R. chinensis.•FM-associated R. chinensis exhibited superior leaf micro-structure under Mn stress than without FM.•FM can alleviate Mn stress by improving osmotic adjustment ability and antioxidative systems.•FM prompted accumulation of inactive forms of Mn in cell wall and vacuoles thereby relieving its toxicity.