Si/GeB multilayers were prepared by ion-beam sputtering technique and the effect of the crystallinity on thermoelectric properties was investigated. The crystallinity of the samples was controlled using Si buffer and SiO2 layers. Samples prepared on the Si buffer layer show similar properties to samples prepared on a Si wafer without the buffer layer. Moreover, it is found that the resistivity of the samples prepared on the Si buffer layer is lower than that of the samples prepared on the Si wafer without the buffer layer because of the surface cleaning effect. On the other hand, samples prepared on SiO2 show poor thermoelectric properties. These results are caused by the change in the crystallinity and periodicity, which are related to the carrier confinement effect. After thermal annealing, it is found that the multilayer structure is degraded rapidly and that the sign of the thermoelectric power is changed. This is considered to be caused by crystalline defects in the interfaces due to the collapse of the multilayer structure.