Effects of Ag doping and thermal annealing temperature on thermoelectric transport properties of Bi2(Se,Te)3 compounds are investigated. On the basis of the comprehensive analysis of carrier concentration, Hall mobility, and lattice parameter, we identified two Ag-related interstitial (Agi) and substitutional (AgBi) defects that modulate in different ways the thermoelectric properties of Ag-doped Bi2(Se,Te)3 compounds. When Ag content is less than 0.5 wt %, Agi plays an important role in stabilizing crystal structure and suppressing the formation of donor-like Te vacancy (VTe) defects, leading to the decrease in carrier concentration with increasing Ag content. For the heavily doped Bi2(Se,Te)3 compounds (>0.5 wt % Ag), the increasing concentration of AgBi is held responsible for the increase of electron concentration because formation of AgBi defects is accompanied by annihilation of hole carriers. The analysis of Seebeck coefficients and temperature-dependent electrical properties suggests that electrons in Ag-doped Bi2(Se,Te)3 compounds are subject to a mixed mode of impurity scattering and lattice scattering. A 10% enhancement of thermoelectric figure-of-merit at room temperature was achieved for 1 wt % Ag-doped Bi2(Se,Te)3 as compared to pristine Bi2(Se,Te)3.