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.