Context. X-ray imaging observatories have revealed hydrodynamic structures with linear scales of similar to 10 kpc in clusters of galaxies, such as shock waves in the 1E0657-56 and A520 galaxy clusters and the hot plasma bubble in the MKW 3s cluster. The future X-ray observatory IXO will for the first time resolve the metal distribution in galaxy clusters at the these scales. Aims. Heating of plasmas by shocks and AGN activities can result in non-equilibrium ionization states of metal ions. We study the effect of the non-equilibrium ionization at linear scales of less than or similar to 50 kpc in galaxy clusters. Methods. A condition for non-equilibrium ionization is derived by comparing the ionization time-scale with the age of hydrodynamic structures. Modeling of non-equilibrium ionization is performed at a point in time when the plasma temperature suddenly changes. An analysis of the relaxation processes of the FeXXV and FeXXVI ions by means of eigenvectors of the transition matrix is given. Results. We conclude that the non-equilibrium ionization of iron can occur in galaxy clusters if the baryonic overdensity delta is smaller than 11.0/tau, where tau << 1 is the ratio of the hydrodynamic structure age to the Hubble time. Our modeling indicates that the emissivity in the helium-like emission lines of iron increases as a result of the deviation from the ionization equilibrium. A slow process of helium-like ionic fraction relaxation was analyzed. A new way to determine a shock velocity is proposed.