We report on the effects of spacer thickness on the external quantum efficiency (EQE) of the solar cells with Ge islands embedded into the intrinsic region of the Si-based p-i-n diode. The EQE response of the solar cells in the near-infrared region is dependent on the spacer thickness that separates the layers of self-assembled Ge islands. It was found that the EQE response has an optimum value when the spacer thickness can sustain a good vertical ordering of islands. On the other hand, random nucleation of islands due to a thicker spacer layer exhibits an inferior EQE response. Furthermore, a drastic decrease of the EQE response of the solar cells for a thinner spacer layer was observed.