The Bi and the Te nano-powders are prepared by inert gas protected evaporation-condensation method; the n-type Bi2Te3 bulk materials with nano-layer and twin crystallite sub-structures are then synthesized by mechanical alloying and spark plasma sintering technique. The effects of grain size and microstructure on thermoelectric property are also systematically studied. The SEM and the TEM analyseis show that the nano-layered Bi2Te3 bulk materials with twin crystallite sub-structures could be fabricated by controlling the preparing procedures. The thermoelectric property result shows that the thermal conductivity is lowered compared with that of bulk material of coarse-grained starting powders. The thermal conductivity decreases from 1.80 W/mK to 1.19 W/mK at 423 K, the lattice thermal conductivity decreases from 1.16 W/mK to 0.61 W/mK at 423 K, indicating that the phonon scattering could be enhanced due to the coexistence of nano-layer and twin crystallite sub-structures, leading to reduced phonon thermal conductivity. The dimensionless figure of merit ZT reaches 0.74 at 423 K for bulk materials sintered at 693 K.