The potential application of monolayer MS2 (M = Mo, W) as thermoelectric material has been widely studied since the first report of successful fabrication. However, their performances are hindered by the considerable band gap and the large lattice thermal conductivity in the pristine 2H phase. Recent discoveries of polymorphism in MS2s provide new opportunities for materials engineering. In this work, phonon and electron transport properties of both 2H and 1T′ phases were investigated by first-principle calculations. It is found that upon the phase transition from 2H to 1T′ in MS2, the electron transport is greatly enhanced, while the lattice thermal conductivity is reduced by several times. These features lead to a significant enhancement of power factor by one order of magnitude in MoS2 and by three times in WS2. Meanwhile, the figure of merit can reach up to 0.33 for 1T′–MoS2 and 0.68 for 1T′–WS2 at low temperature. These findings indicate that monolayer MS2 in the 1T′ phase can be promising materials for thermoelectric devices application. Meanwhile, this work demonstrates that phase engineering techniques can bring in one important control parameter in materials design.