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With the fabrication of high-performance thermoelectric (TE) materials, developments are being made in enhancing the figure of merit, zT, of TE materials. Liquid-like binary copper selenide (Cu2Se) chalcogenides recently gained significant recognition because of their anomalous but fascinating electrical and thermal transport performances. In this study, a facile synthesis technique was adopted in fabricating Cu2Se nanoparticles using a rapid microwave-assisted hydrothermal route at different reaction times. The results were compared with those of the Cu2Se solid-state (SS) sample synthesized using the traditional melting and annealing technique. X-ray diffraction patterns revealed successful synthesis of nanoparticles and a phase transition from orthorhombic α-phase and cubic β-phase to a single orthorhombic structure after hot-pressing. Scanning electron microscopic images revealed that although the grain sizes of the nanoparticle (NP) bulk samples increased with the reaction time of the microwave hydrothermal process, the grain sizes were significantly smaller than that of the SS sample. Additionally, NP bulk samples exhibited plenty of nano-grains and pores that are absent in the SS sample. The size and distribution of the grains and pores were measured to study their effects on the transport of carriers and phonons. The NP30 sample exhibited the highest power factor of 983.3 µW K−2 m at 673 K among the NP samples, exhibiting intermediate values of resistivity and Seebeck coefficient that are close to those of the SS sample. Moreover, the NP samples exhibited appreciably lower thermal conductivity than the SS sample that is attributed to strengthened phonon scattering. The minimum thermal conductivity of the NP05 sample, 0.78 WK−1 m−1 at 348 K, is 1.7 times lower than that of the SS sample. Finally, a maximum zT of 0.56 at 673 K, being approximately 1.3 times higher than that of the SS sample owing to the optimized thermal conductivity, was achieved for the NP30 sample. This value is comparable to or higher than that reported for Cu2Se synthesized using the traditional SS method. Investigations revealed that the proposed microwave hydrothermal synthesis technique is a facile, rapid, and reliable method that results in Cu2Se alloys with excellent TE performance.