Here we present an in-depth and comprehensive study of the effect of the geometry and morphology of nanoarray (NA) substrates on their surface-enhanced Raman scattering (SERS) performance. The high-quality SERS-active NA substrates of various unit shapes and pitches are assembled through electron beam lithography and fabricated by electron beam physical vapor deposition. Good agreement is found on comparing the Raman scattering results with the integrals of the fourth power of local electric fields from the three-dimensional numerical simulations. A novel type of hybrid NA substrate composed of disordered nanoparticles and a periodic NA is fabricated and characterized. The morphology of NAs has little influence on the SERS performance of hybrid NA substrates and they perform better than both their counterparts pure NA and disordered nanoparticle substrates.