Studies aiming to significantly improve thermal properties, such as figure-of-merit, of silicon nanowires (SiNW) have focused on diameter reduction and surface or interface roughness control. However, the mechanism underlying thermal conductivity enhancement of roughness controlled NWs remains unclear. Here, we report a significant influence of stacking faults (SFs) on the lateral thermal conductivity of a single SiNW, using a combination of newly developed in situ spatially-resolved thermal resistance experiments and high-resolution transmission electron microscopy measurements. We used as-grown SiNWs tapered along the growth direction with progressively lower roughness and SFs density. The results clearly confirmed that both surface roughness and twins or SFs densities suppress the thermal conductivity of an individual SiNW. The results and measurement techniques presented here hold great potential for inspecting minute changes in thermal resistance along an individual SiNW, caused by induced SFs on the nanostructure, and for improving one-dimensional nanowire-based thermoelectric device performance.