Directionally solidified alloys in the Ru-Mn-Si system exhibit a particular microstructure including columnar compositional variation due to the formation of many different chimney-ladder phases along the growth direction. Despite the existence of the compositional variation, the crystal orientations of the neighboring chimney-ladder phases are preserved. Over the compositional interfaces, the metal sublattice is considered to be continuous while the Si sublattice is not. Heat treatment of the directionally solidified alloy with the nominal composition of Ru0.10Mn0.90Si1.732 at 1100°C coarsens the compositional domains so as to reduce the density of the compositional interfaces. The values of the thermal conductivity increase with the decrease in the density of the compositional interfaces whereas those of the Seebeck coefficient and electrical resistivity are almost unchanged after the heat treatment. It is considered that the thermoelectric properties of the chimney-ladder compounds in the Ru-Mn-Si system can be enhanced by introducing a high density of the compositional interfaces.