Lattice thermal conductivity ( κ L ) of the hexagon‐shaped nanocrystals cluster of Bi 2 Se 3 , prepared by the hot‐injection technique using nontoxic solvents, is studied. From the temperature‐dependent Raman spectra of Bi 2 Se 3 nanocrystals, the average Debye temperature ( θ D ) and Gruneisen parameter ( γ ) are calculated by adopting the bond‐order–length–strength correlation theory. The average room temperature κ L of Bi 2 Se 3 nanocrystals evaluated from the Slack model using θ D and γ is ≈1.1 Wm −1 K −1 . The κ L of Bi 2 Se 3 nanocrystals is larger than out‐of‐plane κ L (≈0.4 Wm −1 K −1 ) but close to the in‐plane κ L (≈1.4 Wm −1 K −1 ) simulated using the Boltzmann transport equation for phonon with three‐phonon scatterings. Nanostructuring introduces grain boundaries in the Bi 2 Se 3 that block the long mean free path of phonons physically, reduces the phonon mean free path, and decreases the κ L . The anisotropic phonon scattering introduced by the weak van der Waals force between adjacent quintuple layers in the out‐of‐plane direction, in addition to the acoustic–optical phonon scattering and anharmonicity, hinders the efficient transport of thermal energy in the Bi 2 Se 3 and results in a lower κ L . By utilizing materials with anisotropic thermal conductivity, thermoelectric devices can be designed to preferentially conduct heat in specific directions while minimizing heat loss in others.