Surface-enhanced Raman scattering (SERS)-based sensing is the most promising approach to detect trace amounts of chemical and biological molecules. Three-dimensional (3D) nanostructures have been considered as one of the most promising SERS substrates due to ordered arrangement of high-density hot spots and large surface area for adsorbing analyte. This paper designed a hybrid SERS substrate containing structures of Fe3O4 and Ag nanoparticles on Si nanopillar arrays, which combines the advantages of highly ordered periodic 3D Si nanopillar arrays and Ag coated Fe3O4 core-satellite micro spheres, leading to intense light metal and light molecule interactions. The detection limit of the substrate for malachite green (MG) is as low as 10(-8) M, meeting the requirements for trace detection of analytes. This work provides a new insight for fabricating SERS substrates with high sensitivity. (C) 2018 Elsevier B.V. All rights reserved.