In the thermoelectric field, GeSe is a two-dimensional layered semiconductor with a large band gap, intrinsically low carrier concentration and poor thermoelectric figure of merit ZT. In this work, a series of GeSe _1–xTe _x( x= 0, 0.05, 0.15, 0.25, 0.35, 0.45) polycrystalline samples is prepared by melting and quenching combined with spark plasma activation sintering process. The influences of Te content on the phase structure and thermoelectric transport properties of GeSe are systematically studied. The results indicate that with the increase of Te content, the crystal structure of GeSe gradually changes from orthorhombic to rhombohedral structure. This reduces the band gap of the material, and simultaneously increases the carrier concentration and mobility. Meanwhile, the energy band degeneracy of the compound increases significantly because of enhanced crystal symmetry in this process, thereby considerably improving the effective mass of carriers. Altogether, the power factor of the rhombohedral GeSe is increased by about 2 to 3 orders of magnitude compared with that of the orthorhombic phase GeSe. In addition, the rhombohedral phase GeSe has abundant cationic vacancy defects and softened phonons arising from its ferroelectric feature, leading the lattice thermal conductivity to be 60% lower than orthorhombic one. The GeSe _0.55Te _0.45sample achieves a peak ZTof 0.75 at 573 K, which is 19 times that of pristine GeSe. Crystal structure engineering could be considered as an effective way of improving the thermoelectric performance of GeSe compounds.