Context : X-ray imaging observatories have revealed hydrodynamic structures with linear scales \sim 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 resolve for the first time 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 \lesssim 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 when the plasma temperature suddenly change is performed . An analysis of 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 \ll 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 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 . Conclusions :