We investigated the effects of arbuscular mycorrhizal fungus inoculation on net ion flux in the roots of trifoliate orange (Poncirus trifoliata (L.) Raf.) and mineral nutrition in seedlings under zinc contamination. A pot experiment was conducted to study plant growth as well as the distribution of zinc, copper, phosphorus, potassium, calcium, and magnesium in trifoliate orange seedlings inoculated by the arbuscular mycorrhizal fungus, Glomus intraradices, under greenhouse conditions. Plants were grown in yellow soil:quartz sand (9∶1, v/v) medium and were irrigated with solutions containing three different zinc concentrations (0, 300 and 600 mg/kg), which corresponded to control, medium and high zinc contamination treatments, respectively. Meanwhile, a non-invasive micro-test technique was used to determine the net fluxes of Ca²⁺, H⁺ and NO₃^- along mycorrhizal and non-mycorrhizal roots of trifoliate orange seedlings grown in medium with no zinc added. Arbuscular mycorrhizal colonization significantly increased the fresh weight of shoots and roots exposed to different zinc levels. With increasing zinc concentrations, the mycorrhizal colonization percentage decreased, while the zinc levels in the shoots and roots progressively increased. Zinc concentrations in the roots were significantly higher in arbuscular mycorrhizal seedlings than in non-arbuscular mycorrhizal seedlings. The shoot/root ratios of the zinc translocation coefficient gradually decreased in arbuscular mycorrhizal seedlings with increasing zinc concentrations. This indicated that at medium or high levels of zinc contamination, a lot of zinc was immobilized in roots through the establishment of mycorrhizae. Therefore, phytotoxicity might be alleviated. Copper, phosphorus, potassium, and magnesium concentrations in shoots of plants grown in medium with no added zinc were significantly higher in arbuscular mycorrhizal seedlings than those in non-arbuscular mycorrhizal seedlings. Similarly, copper concentrations in the roots of plants in medium with 600 mg/kg of added zinc and phosphorus concentrations in roots of plants in medium with 300 mg/kg added zinc were higher in arbuscular mycorrhizal seedlings. Arbuscular mycorrhizal colonization had no significant effects on calcium concentrations in seedlings. Copper and phosphorus concentrations gradually decreased in both arbuscular mycorrhizal and non-arbuscular mycorrhizal seedlings with increasing zinc levels, which demonstrated that zinc levels in seedlings are negatively correlated with copper or phosphorus. With no added zinc, phosphorus, potassium, magnesium and copper uptake was promoted by arbuscular mycorrhizal fungus infection. Under zinc contamination, phosphorus, and copper uptake was still accelerated by mycorrhizal colonization. Thus, the effects of mycorrhizal colonization were not only related to the degree of zinc pollution, but were also correlated with the species of fungi and host plants. Additionally, net Ca²⁺ efflux at 0 μm and 600 μm, net H⁺ influx at 600 μm, and net NO₃^- influx at 2400 μm from the root tip of arbuscular mycorrhizal seedlings in medium with no added zinc were significantly higher than those of non-arbuscular mycorrhizal seedlings. These results suggest that mycorrhizal symbiosis activates Ca²⁺-ATPase, Ca²⁺/H⁺ antiporters and NO₃^-/H⁺ symporters in root plasma membranes. Nutrient uptake and stimulation of growth are mediated by arbuscular mycorrhizal fungi. Furthermore, the variations detected in arbuscular mycorrhizal roots for Ca²⁺, H⁺ and NO₃^- fluxes point to a significant involvement of the fungus.