In this report, the thermoelectric properties of a Bi0.8Sb1.2Te2.9 nanowire (NW) were in-situ studied as it was trimmed from 750 down to 490 and 285 nm in diameter by a focused ion beam. While electrical and thermal conductivities both indubitably decrease with the diameter reduction, the two physical properties clearly exhibit different diameter dependent behaviors. For 750 and 490 nm NWs, much lower thermal conductivities (0.72 and 0.69 W/m-K respectively) were observed as compared with the theoretical prediction of Callaway model. The consequence indicates that in addition to the size effect, extra phonon scattering of defects created by Ga ion irradiation was attributed to the reduction of thermal conductivities. As the NW was further trimmed down to 285 nm, both the electrical and thermal conductivities exhibited a dramatic reduction which was ascribed to the formation of amorphous structure due to Ga ion irradiation. The size dependence of Seebeck coefficient and figure of merit (ZT) show the maximum at 750 nm, then decrease linearly with size decrease. The study not only provides the thoroughly understanding of the size and defect effects on the thermoelectric properties but also proposes a possible method to manipulate the thermal conductivity of NWs via ion irradiation.