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In this study, single crystals of Tr<i>_x</i>Bi₂Se₃ (Tr = Co, Fe, and Mn) were produced via a melt-grown reaction. All crystals are <i>c</i>-axis oriented with an excellent single crystalline phase. The smaller ionic radius of the transition metal elements makes the QLs of Bi₂Se₃ thinner. Their abundant magnetism will provide spin–phonon coupling channels when the phonons are scattering in the system. Both Stokes and anti-Stokes Raman spectroscopy were performed for the three optical phonon modes of the Bi₂Se₃ crystals. These peaks were centered at 74.5 cm⁻¹, 133.4 cm⁻¹, and 175.2 cm⁻¹ and were attributable to the <i>A_1g</i>(1), <i>E_g</i>(2), and <i>A_1g</i>(2) modes, respectively. With an increase in the doping concentration, the magnetic and compressive strains induced by impurities dominate the phonon dynamics of materials. The results provide an effective scheme to regulate the thermoelectric properties of a Bi₂Se₃ system.