Nano porous silicon (PS) is a strong candidate for thermoelectric application, but it shows low structural stability and is prone to collapse. To enhance the structural stability of PS and offer a new way to improve its electrical conductivity, PS was prepared by electrochemical etching and Bi nanowires were fabricated in the pores of PS by electrodeposition. In addition, for studying the effect of structures on the properties of Bi-filled PS composites, aperiodic single-layer (SL) structure, and periodic rugate (Rgt) structure and Bragg structure PS samples were prepared by changing the etching current waveform and etching time. The results show that the initial Bi deposition position and filling fraction of Bi nanowires in PS templates can be precisely controlled. Since Bi nanowires have significantly different continuity in Rgt and Bragg structures compared with SL structures, we proposed two growth mechanisms of Bi nanowires, including the axis-growth mechanism and transverse-axis-growth mechanism, with the supports of the experimental results of XRD, SEM, and EDS.The room temperature thermal conductivities of pristine and Bi-filled PS layers are in the ranges of 4.5 ∼ 5.0 and 4.2 ∼ 6.0 W・m−1K−1, respectively, about 1/10 of the original unetched silicon wafer. No apparent increase of thermal conductivity was observed in any Bi-filled composites. In addition, the thermal conductivities of PS layers with Bragg structure, including pristine and Bi-filled PS composites, are significantly lower than those of the other two structures.SEM images also demonstrates that Bi greatly improved the mechanical property of PS composites, especially the periodic structures composites. This study firmly demonstrates that Bi-filling in PS with periodic Bragg structure is practical to obtain nanocomposites with low thermal conductivity and improved structural stability. It offers a new dimension to optimize the property of PS for thermoelectric application by pore configuration design and controllable nanowire Bi filling.