The metal nanoparticles exhibit different degrees of localized surface plasmon resonance which depends on different type nano-sized structures. In this work, in experiment, Au/TiO2/Ti/Si SERS-active substrate with spherical shape nanoparticles is fabricated by using a hydrothermal treatment process and applied to detect Rhodamine 6G sample. Based on experimental observation, a three-dimensional finite-difference time-domain simulation is utilized to explore the local field distributions. We examine the effect of surface roughness and shape of Au nanoparticles on the enhancement magnitude of local electric field of SERS-active substrates. Besides, different shapes of nanoparticles, nanocages and Au/Ag alloy nanoparticles are also modeled and discussed. The engineering findings of this study indicate that the substrate with roughened surface may exhibit large electric field enhancement; in particular, for the cubic shape of nanoparticles. The electric field enhancement of spherical and cubic nanoparticles could be further enlarged by Au/Ag alloy and Au nanocage structures. The results may benefit the design and fabrication of nanoparticles for various biochemical sensing applications.