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 GeSe1-xTex (x=0, 0.05, 0.15, 0.25, 0.35, 0.45) polycrystalline samples were prepared by melting, quenching combined with spark plasma activation sintering process. The influences of Te content on the phase structure and thermoelectric transport properties of GeSe were systematically studied. The results indicate that, with the increase of Te content, the crystal structure of GeSe gradually changes from orthorhombic to rhombohedral. This reduces the band gap of the material, and simultaneously increases the carrier concentration and mobility. Meanwhile, the energy band degeneracy of the compound gets significantly increased because of enhanced crystal symmetry during this process, thereby considerably boosting the effective mass of carriers. Altogether, the power factor of the rhombohedral GeSe is increased by about 2 to 3 orders of magnitude compared to the orthorhombic phase GeSe. In addition, the rhombohedral phase GeSe has abundant cationic vacancy defects and softened phonons arising from its ferroelectric feature, leading to 60% lower lattice thermal conductivity than orthorhombic one. GeSe0.55Te0.45 sample achieves a peak ZT of 0.75 at 573 K, which is 19 times that of pristine GeSe. Crystal structure engineering could be considered as an effective way of elevating the thermoelectric performance of GeSe compounds