The alloying effect of ZrO2 on the microstructure of the thermoelectric material, TinO2n−1, which is a partially reduced rutile phase called the Magnèli phase, is investigated. The microstructure of TinO2n−1 is characterized by periodically induced planar defects, called shear planes, in the rutile matrix. The configuration of the O atoms around a Ti atom in a shear plane is different from that in the rutile matrix but similar to that in Ti2O3. It is speculated that the alloying of ZrO2, which has an equivalent structure to that of rutile, causes preferential Zr addition in the rutile matrix. From the microstructural observation of the alloying specimen (Ti10O19+6 mol%ZrO2), it is revealed that the added Zr is distributed homogeneously in the entire microstructure because the valence of the Ti atoms in the matrix rutile and shear plane is similar.