In this study, hexagonal-packed Si nanorods (SiNRs) arrays were fabricated and conjugated with Au nanoparticles (AuNPs) in different spatial distributions for surface-enhanced Raman spectroscopy (SERS). The AuNPs were functionalized on the bottom of SiNRs (B-SiNRs@AuNPs), top of SiNRs (T-SiNRs@AuNPs) and sides of SiNRs (S-SiNRs@AuNPs), respectively. Our results demonstrated that the SiNRs conjugated with AuNPs on the sides achieved high reproducibility in detection of R6G molecules, while the AuNPs on the top of the SiNRs obtained the strongest Raman enhancement. In addition, the substrate with S-SiNRs@AuNPs obtained the highest spatial uniformity of enhancement. The finite-difference time-domain simulation gave further evidence that the incident light could be confined in the space of SiNRs arrays and yield a zero-gap enhancement coupled with the AuNPs. Our study provided a spatially tunable SiNRs@AuNPs substrate with high sensitivity and reproducibility in molecular detection.