Kagome metal ScV6Sn6 has been a subject of interest due to the emergence of a first-order structural phase transition with intriguing charge density wave behavior below the transition temperature Tc ∼ 92 K. To explore the thermoelectric properties and provide experimental insights into the nature of the phase transition, we have carried out a combined study by means of the electrical resistivity, Seebeck coefficient, and thermal conductivity measurements on single crystalline ScV6Sn6. Pronounced features near Tc have been characterized by all measured physical quantities. In particular, the Seebeck coefficient exhibits a marked reduction as lowering temperature across Tc, attributed to an imbalance of the contribution from different type of carriers induced by the structural phase transition. From the examination of the electronic and lattice thermal conductivities, we obtained a confirmation that the observed enhancement at Tc is essentially caused by the change of the lattice thermal conductivity, demonstrating the primary importance of lattice distortions for the heat transport of ScV6Sn6. In addition, the lattice thermal conductivity above Tc was found to increase monotonically with temperature. We associated the peculiar phenomenon with lattice fluctuations, highlighting the essence of structural instability in the kagome lattice ScV6Sn6. These results add to the knowledge about the thermal transport properties in kagome materials with a hexagonal HfFe6Ge6-type structure.