The assembly of 2D materials via vertical stacking has shown great advantages in modern device design, while the interface formed by two 2D materials also provides a new opportunity to tune various physical properties. Herein, the impact of homogeneous stacking on the thermal conductivity of 2D SnSe, a promising thermoelectric material, has been elucidated by solving the phonon‐Boltzmann transport equation with the first‐principles approach. SnSe bilayer and trilayer stacks, involving diverse interfacial configurations, are constructed to reveal potential modulation of in‐plane lattice thermal conductivity. Compared to the single‐layer counterpart, the result demonstrates a reduced thermal transport capacity in both the SnSe bilayer and trilayer due to van der Waals interaction, and the SnSe bilayer could exhibit a greater potential for thermoelectric applications due to the significantly suppressed phonon transport. Moreover, the interface effect can be further verified by the stacking‐dependent behavior of thermal conductivity, while the reduced thermal conductivity in SnSe stacks can be attributed to the decreased phonon relaxation time caused by interlayer interactions, implying great potential to further promote 2D SnSe‐based thermoelectric applications by stacking modulation.