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Reduction of thermal conductivity is essential for obtaining high energy conversion efficiency in thermoelectric materials. We report on significant reduction of thermal conductivity in niobium-doped CaO(CaMnO3)m compounds for thermoelectric energy harvesting due to introduction of extra CaO-planes in the CaMnO3-base material. We measure the thermal conductivities of the different compounds applying the laser flash analysis at temperatures between 300 and 1000 K, and observe a remarkable reduction in thermal conductivity with increasing CaO-planar density, from a value of 3.7 W·m−1K−1 for m = ∞ down to 1.5 W·m−1K−1 for m = 1 at 400 K. This apparent correlation between thermal conductivity and CaO-planar density is elucidated in terms of boundary phonon scattering, providing us with a practical way to manipulate lattice thermal conductivity via microstructural modifications.