This study used a rapid and simple microwave-assisted synthesis method to grow ZnO nanoneedle arrays on the silicon substrate with the ZnO seed layer. The effects of reaction temperature and time on the lengths of ZnO nanoneedle arrays were investigated. The appropriate temperature programming step can grow the longer ZnO nanoneedle arrays at the same reaction time (25 min), which is 2.08 times higher than without the temperature programming step. The geometry of the ZnO nanoneedle arrays features a gradual decrease from the Si substrate to the surface, which provides an excellent progressive refractive index between Si and air, resulting in excellent antireflection properties over an extensive wavelength range. In addition, the ZnO nanoneedle arrays exhibit a suitable structure for uniform deposition of Ag nanoparticles, which can provide three-dimensional hot spots and surface active sites, resulting in higher surface-enhanced Raman scattering (SERS) enhancement, high uniformity, high reusability, and low detection limit for R6G molecule. The ZnO/Ag nanoneedle arrays can also reveal a superior SERS-active substrate detecting amoxicillin (10-8 M). These results are promising for applying the SERS technique for rapid low-concentration determination in different fields.