Bi₂Te₃-based compounds have attracted great attention in near-room-temperature thermoelectric applications because of their excellent electrical transport properties and low thermal conductivity. Solid solutions and doping can effectively optimize the performance of Bi₂Te₃-based materials. Currently, n-type Bi₂Te_3–x Se_x materials doped with selenium (Se) have been reported. However, the regulatory mechanisms of Se doping directly at Te sites on their defect structure, microstructure, and bandgap have not yet been systematically investigated. This work systematically investigates the regulatory behavior of Se doping directly at Te sites on the defect structure, microstructure, and bandgap of ternary n-type Bi₂Te_3–x Se_x compounds, and its influence on thermoelectric transport properties. The Se substitution at Te sites forms n-type donor defects \textSe_\textTe^\text• , inhibits the formation of Bi′Te antisite defects, and facilitates the return of Bi atoms to their intrinsic lattice sites, while introducing Te interstitial atoms ( \textTe_\mathrmi^\times ) and Te vacancies ( \textV_\textTe^\text•• ) and optimizing both carrier concentration and mobility, thereby effectively enhancing the electrical performance. Furthermore, supersaturated Te diffuses out as interstitial atoms and precipitates to form secondary phases. Se doping enhances phonon scattering via mass and strain field fluctuations induced by point defects, leading to a significant reduction in lattice thermal conductivity. As x increases, the bandgap of the sample is widened, resulting in significant suppression of the performance degradation caused by the intrinsic-excitation-induced bipolar effect. Consequently, the Bi₂Te_2.7Se_0.3 sample achieves a maximum average zT (zT_ave) value of 0.73 in a temperature range of 300–500 K. After annealing, the optimization of the sample’s microstructure leads to an enhanced power factor and reduced thermal conductivity in the Bi₂Te_2.4Se_0.6 sample, achieving a maximum zT value of 0.81 at 420 K and a zT_ave value of 0.76 in the temperature range of 300–500 K. These results demonstrate that Se doping directly at Te sites can broaden the temperature range corresponding to the optimal zT values, and that the annealing process can further optimize the thermoelectric performance. This study provides significant insights for developing high-performance near-room-temperature thermoelectric materials applicable to broad operating temperatures.