The paper demonstrates a simple way to control the filling degree of the pores of a silicon oxide template on silicon substrate with nickel. SiO2/Si template was formed using the swift heavy ion tracks technology, which includes irradiation with high energy ions and chemical transformation of the obtained latent tracks into the pores. The preparation of SiO2(Ni)/Si nanostructures with different filling degree of pores in SiO2 with nickel was performed using the electrodeposition method by changing the duration of the process. A study and analysis of the morphology of SiO2(Ni)/Si nanostructures using scanning electron and atomic force microscopy was carried out to determine the nature of pore filling by metal.