In this study, large-area hexagonal-packed Si nanorod (SiNR) arrays in conjunction with Au nanoparticles (AuNPs) were fabricated for surface-enhanced Raman spectroscopy (SERS). We have achieved ultrasensitive molecular detection with high reproducibility and spatial uniformity. A finite-difference time-domain simulation suggests that a wide range of three-dimensional electric fields are generated along the surfaces of the SiNR array. With the tuning of the gap and diameter of the SiNRs, the produced long decay length (>130 nm) of the enhanced electric field makes the SERS substrate a zero-gap system for ultrasensitive detection of large biomolecules. In the detection of R6G molecules, our SERS system achieved an enhancement factor of >107 with a relative standard deviation as small as 3.9-7.2% over 30 points across the substrate. More significantly, the SERS substrate yielded ultrasensitive Raman signals on long amyloid-β fibrils at the single-fibril level, which provides promising potentials for ultrasensitive detection of amyloid aggregates that are related to Alzheimer's disease. Our study demonstrates that the SiNRs functionalized with AuNPs may serve as excellent SERS substrates in chemical and biomedical detection.