Thermoelectric materials are actively considered for waste heat recovery applications. To improve the heat to electricity conversion efficiency, fundamental understanding on composition, crystal structure, and interrelation with the thermoelectric properties is necessary. Here, we report the chemical and thermoelectric properties of type-I clathrates Ba8Ni3.8SixGe42.2−x (x = 0, 10, 20, 42.2), to show that the Si substitution can retain the low lattice thermal conductivity as in pure Ge-based clathrates by adding defects (cage distortion) scattering and/or alloying effect, and the charge carrier concentration can be optimized and thus the electronic properties can be improved by tailoring the vacancy content. We demonstrate the vacancies in the pure Ge-based compound by Rietveld refinement, and possible vacancies in the quaternary compound by transport property measurements. We also show that, for intrinsic property studies in these compounds with such a complex crystal structure, a heat treatment for as cast alloys is necessary for phase purity and composition homogeneity. The highest ZT value of 0.19 at 550 °normalC is reached in the compound with x=10.