Considering the complex hydrogeology condition and the particularity of mineral composition of shallow brackish aquifers for energy storage, a controllable three-dimension infiltration experiment is conducted. Based on the theories of surface chemistry and colloid stability, the intrinsic connection between the variation of macro parameters of recharged solutions and the redistribution of micro-nano particles are analyzed from the mesoscopic standpoint. The spatial and temporal variations of the pore structure of brackish aquifer are analyzed; and the regions of low permeability curtain formed in different modes are determined. The results show that it is the variation of temperature and salinity of recharge solution that breaks equilibrium condition of forces between particles and induces the decrease of aquifer medium permeability. By fixing and switching the locations of pumping and injection well, the relative permeability of the whole aquifer medium k/k0 decrease to 63% and 57%, respectively, after one complete energy storage period, showing that the aquifer medium space structure variations are irreversible as result of micro-nano particles redistribution. Under the two working modes, low permeability curtain occurs in the 700-900 mm and the 500-700 mm seepage elements, respectively, due to their different formation mechanism.