Thermoelectric Bi2Te3 alloy nanopowders with different morphologies were synthesized by hydrothermal processes with different surfactants. The nanopowders were hot-pressed into pellets, and their thermoelectric properties were investigated. The results show that the morphologies of the nanopowders have remarkable effects on the thermoelectric properties of the hot-pressed bulk pellets. A suitable microstructure of the bulk pellet prepared from flower-like nanosheets was found, having a lower electrical resistivity, larger Seebeck coefficient, and lower thermal conductivity, resulting in a high figure of merit ZT ≈ 1.16. The effects of the nanopowders with different morphologies on the microstructure and thermoelectric properties of hot-pressed bulk pellets are discussed.