Heat conduction in ceramics is attributed to phonon propagation, which can be strongly suppressed at boundaries. Usually, polycrystals show lower thermal conductivity (κ) than single crystals, as polycrystals contain many grain boundaries. For functional applications in thermal management technologies, ceramics with low thermal conductivity are required. While grain boundary engineering is effective for reducing κ, its utilization is limited by the fact that other functional properties are often damaged. Here it is shown that single‐crystalline oxide of InGaO3(ZnO)m with a natural superlattice structure exhibits anomalously lower κ than polycrystals. Single‐crystalline films of InGaO3(ZnO)m (m = integer), which has a superlattice structure of InO2−/GaO(ZnO)m+ stacking along the c‐axis with a controllable layer thickness of m, are fabricated. It is found that the κ perpendicular to the superlattices decreases with decreasing m‐value, and the minimum κ is 1.1 W m−1 K−1 (m = 4, 5), which is lower than randomly oriented polycrystalline InGaO3(ZnO)m. On the other hand, the κ parallel to the superlattices have similar values with those of polycrystalline. The present finding suggests that layer boundaries between different components inside single crystal can also function as thermal resistance, which will be useful for the material design of thermal management technologies.