Bi<sub>2</sub>Te<sub>3</sub>-based compounds are the best performing thermoelectric materials near room temperature. The presence of numerous complex defects renders defect engineering as the core stratagem for modulating and improving the thermoelectric performance.Therefor rationally understanding and effectively controlling the existence form and concentration of defects are crucial for achieving high-thermoelectric performance in Bi<sub>2</sub>Te<sub>3</sub>-based alloys.Herein, a series of Cl doped n-type quaternary Bi<sub>2-x</sub>Sb<sub>x</sub>Te<sub>3-y</sub>Se<sub>y</sub> compounds were synthesized by zone-melting method. The correlation between defect evolution process and thermoelectric performance were systematically investigated by first-principles calculation and experiments.Alloying Sb on Bi site and Se on Te site induce charged structural defects, leading to a significant change in the carrier concentration.For Bi<sub>2-x</sub>Sb<sub>x</sub>Te<sub>2.994</sub>Cl<sub>0.006</sub> compounds, alloying Sb on Bi site decreases the formation energy of the <i>S</i>b<sub>Te<sub>2</sub></sub> antisite defect,which generates the antisite defect SbTe 2 and accompanies with the increase of the minority carrier concentration from 2.09×10<sup>16</sup>cm<sup>-3</sup> to 3.99×10<sup>17</sup>cm<sup>-3</sup>.The increase of the minority carrier severely deteriorates the electrical transport properties. In contrast, alloying Se in the Bi<sub>1.8</sub>Sb<sub>0.2</sub>Te<sub>2.994-y</sub>Se<sub>y</sub>Cl<sub>0.006</sub> compounds significantly lowers the formation energy of the complex defect <i>S</i>e<sub>Te<sub>+<i>S</i>b<sub>Bi<sub>,which becomes more energetically favorable and suppresses the formation of the antisite defect SbTe 2. As a result,the concentration of minority carriers decreases to 1.46×10<sup>16</sup>cm<sup>-3</sup>.This eliminates the deterioration effect of the minority carrier on the electrical transport properties of the material and greatly boosts the power factor.A maximum power factor of 4.49 mW m-1 K-2 is achieved for Bi<sub>1.8</sub>Sb<sub>0.2</sub>Te<sub>2.944</sub>Se<sub>0.05</sub>Cl<sub>0.006</sub> compound at room temperature.In conjunction with the reduced thermal conductivity by intensified phonon scattering via alloying Sb and Se, the maximum <i>ZT</i> value of 0.98 is attained for Bi<sub>1.8</sub>Sb<sub>0.2</sub>Te<sub>2.844</sub>Se<sub>0.15</sub>Cl<sub>0.006</sub> compound at room temperature.Our finding provides an important guidance for modulating point defects, carrier concentration, and thermoelectric performance in Bi<sub>2</sub>Te<sub>3</sub>-based compounds with complex compositions.