Zinc (Zn) is an essential microelement involved in various plant physiological processes. However, in excess, Zn becomes toxic and represents serious problem for plants resulting in Zn toxicity symptoms and decreasing biomass production. The effect of high Zn and its combination with silicon (Si) on ionome and expression level of ZmLsi genes was investigated in maize (Zea mays, L; hybrid Novania). Plants were cultivated hydroponically in different treatments: control (C), Zn (800 μM ZnSO₄ · 7H₂O), Si5 (5 mM of sodium silicate solution), and Si5 + Zn (combination of Zn and Si treatments). Growth of plants cultivated for 10 days was significantly inhibited in the presence of high Zn concentration and also by Zn and Si interaction in plants. Based on principal component analysis (PCA) and mineral element concentration in tissues, root ionome was significantly altered in both Zn and Si5 + Zn treatments in comparison to control. Mineral elements Mn, Fe, Ca, P, Mg, Ni, Co, and K significantly decreased, and Se increased in Zn and Si5 + Zn treatments. Shoot ionome was less affected than root ionome. Concentration of shoot Cu, Mn, and P decreased, and Mo increased in Zn and Si5 + Zn treatments. The PCA also revealed that the responsibility for ionome changes is mainly due to Zn exposure and also, but less, by Si application to Zn stressed plants. Expression level of Lsi1 and Lsi2 genes for the Si influx and efflux transporters was downregulated in roots after Si supply and even more downregulated by Zinc alone and also by Zn and Si interaction. Expression level of shoot Lsi6 gene was differently regulated in the first and second leaf. These results indicate negative effect of high Zn alone and also in interaction with Si on Lsi gene expression level and together with ionomic data, it was shown that homeostatic network of mineral elements was disrupted and caused negative alterations in mineral nutrition of young maize plants.