GeTe has become a high-performance thermoelectric material with a figure of merit (ZT) over two through alloying and band engineering strategies. Yet, the question on how to effectively engineer the electronic band structure of GeTe toward achieving a better thermoelectric performance still cannot be clearly answered, and its underlying physics has not been well understood. Here, we manipulate the lattice structure of GeTe via modifying the lattice parameters, interaxial angles and reciprocal displacements, and investigate their influence on the electronic band structure and thermoelectric properties using first-principles calculations. The calculation results show that the reciprocal displacement directly manipulates the energy level of the L-band and the Z-band, resulting in an indirect–direct transition of the band gap and a strong Rashba effect. Modifications of lattice parameters and interaxial angles can affect band gaps, band convergence and density of states, which are crucial to determining thermoelectric performance. This work performs a systematic study on how the lattice structure manipulation influences the electronic band structure and thermoelectric properties of GeTe, and can provide a clear route to further enhance its ZT.