The influence of shallow surface nanoholes on the growth direction of silicon nanowires (SiNWs) with the vapor–liquid–solid (VLS) process was studied in order to realize a single-step way to promote integration of high-density SiNWs along a specific direction. Shallow surface nanoholes were formed by the short-time metal-assisted chemical etching (MACE) process with catalytic Au nanoparticles of 60 nm also used for the VLS process, in order to shape nanoholes with a similar diameter to the nanoparticles. With an increase in MACE processing time to 5 min, the ratio of perpendicularly grown SiNWs to the SiNWs that appeared on the (111) silicon surface significantly increased in the initial growth phase, reaching higher than 80%. This ratio was more than 3 times higher than without the MACE process. On the other hand, the excess processing time brought about a decrease of the SiNWs detected. This result indicated that the formation of surface nanoholes with an appropriate depth could be an effective way of controlling SiNW growth direction.