In van der Waals (vdW) layered thermoelectric materials, stacking faults play a pivotal role in determining their physical and transport properties. However, the absence of effective methods to control these stacking faults has hindered the optimization of transport performance. Here, in situ mechanical transmission electron microscopy techniques are applied to a state-of-the-art vdW thermoelectric compound, SnSe, to manipulate the generation of stacking faults. A comprehensive analysis of the atomic structure of stacking faults is conducted, and energy barrier calculations reveal the slip pathways of interlayer slips inducing these stacking faults. Furthermore, first-principles calculations demonstrate that introducing stacking faults can enhance thermoelectric performance by promoting band convergence and facilitating charge transport. These results provide a comprehensive understanding of stacking faults and present distinctive opportunities for structure manipulation to enhance functional properties in vdW layered materials.