We report thermoelectric (TE) properties of topological surface Dirac states (TSDS) in threedimensional topological insulators (3D-TIs) purely isolated from the bulk by employing single crystal Bi2-xSbxTe3-ySey films epitaxially grown in the ultrathin limit. Two intrinsic nontrivial topological surface states, a metallic TSDS (m-TSDS) and a gap-opened semiconducting topological state (g-TSDS), are successfully observed by electrical transport, and important TE parameters (electrical conductivity (σ), thermal conductivity (κ), and thermopower (S)) are accurately determined. Pure m-TSDS gives S=-44 μVK -1 , which is an order of magnitude higher than those of the conventional metals and the value is enhanced to -212 μVK -1 for g-TSDS. It is clearly shown that the semi-classical Boltzmann transport equation (SBTE) in the framework of constant relaxation time (τ) most frequently used for conventional analysis cannot be valid in 3D-TIs and strong energy dependent relaxation time τ(E) beyond the Born approximation is essential for making intrinsic interpretations. Although σ is protected on the m-TSDS, κ is greatly influenced by the disorder on the topological surface, giving a dissimilar effect between topologically protected electronic conduction and phonon transport.