It is shown that the magnetoresistive properties of n–Si/SiO2/Ni, nanostructures containing nanogranular nickel rods in a SiO2 layer’s vertical pores substantially differ from the similar properties in the earlier studied nanogranular Ni films electrodeposited onto the n–Si plates. From the point of view of the electrophysical properties, the nanostructures studied are analogous to a system of two Schottky Si/Ni diodes, which are connected to each other. The magnetoresistance of such structures has been studied in the temperature range from 2 to 300 K and the magnetic field range of up to 8 Tl. It is established that at temperatures of 17–27 K the structures possess a positive magnetoresistive effect, whose value depends on the transverse voltage applied to the structure and increases with a decrease in the longitudinal (along the rods) current intensity. At a current of 100 nA, the relative magnetoresistance in the field of 8 Tl increases from 500 to 35000% by an increase in the transverse voltage from 0 to–2 V. The observed magnetoresistive effect is associated with the influence of the magnetic field on the processes of impact ionization of impurities resulting in an avalanche breakdown of the Ni/Si Schottky barrier. Thus, the possibility of controlling the magnetoresistive effect in n–Si/SiO2/Ni template structures by applying an additional (transverse) electric field to the nanostructure between the silicon substrate (as the third electrode) and nickel rods is proven.