The micronutrient zinc plays an essential role in the physiological and metabolic processes in plants; however, it becomes very toxic when present in elevated amounts. To evaluate the correlation of metal tolerance proteins (MTP) with Zn accumulation and distribution in Malus halliana seedlings under zinc toxicity stress, seedlings with 8 true leaves were exposed to different Zn concentrations (4, 25, 50, 100 μmol·L−1) in a hydroponic culture system. We found that excessive Zn stress leads to a decrease in plant growth indexes and the accumulation and distribution of Zn in Malus halliana. With increasing levels of Zn stress, the Zn concentration in roots was significantly higher than in stems and leaves. At 100 μmol·L−1 Zn, the Zn concentration in roots, stems and leaves increased by 45.88, 26.51 and 25.43-fold when compare to CK, respectively. The increase of bioaccumulation factor (BAF) and the decrease of translocation factor (TF) all indicated that Zn was accumulated in the roots. Correlation and hierarchical clustering analysis found that the expression of MTP genes is closely associated with Zn concentrations. The MTP2, MTP11 and MTPC2-like genes were significantly negatively correlated with Zn concentration in roots and were resistant to excessive Zn concentration and sequestration. The expression of MTP1 had organ-specificity that was significantly higher in stems and leaves than that in roots. The expression of MTPC4-like was significantly positively correlated with Zn concentration under the treatment of 4 μmol·L−1 Zn, but the correlation decreased under the high concentration of Zn stress, which indicated that the expression of MTP gene was affected by Zn concentration.