Zinc (Zn) is an important higher plant micronutrient; however, high amounts of Zn in soil may negatively affect plant growth. In this study, two wheat (Triticum aestivum L.) genotypes [Aikang58 (AK) and Zhengmai0856 (ZM)] were grown in nutrient solutions containing various Zn concentrations and were characterized using physiological and molecular approaches. Compared to sufficient Zn supply (0.25 mg L−1), excess Zn (2.5 mg L−1) significantly decreased the biomass and root morphological features (root length, volume, and surface area) of AK, whereas only a slight decrease was observed in ZM. ZM maintained higher Zn concentration and translocation factor, and lower net photosynthetic rate than AK under excess Zn supply. Excess Zn decreased Cu, Fe, and Mn concentrations in roots of both wheat genotypes, whereas Mn concentrations in shoots increased. In addition, the expression of TaZIPs indicated that TaZIP5, −6, and −13 in roots are primarily involved in Zn uptake when the medium has elevated Zn levels. The translocation of more Zn from the roots to shoots facilitates in maintaining the efficiency of photosynthesis by using lower amounts of photosynthetic pigments, and TaZIP genes involved in cell ion homeostasis contributes to greater Zn tolerance in ZM than AK.