SAW devices with a multi-layered piezoelectric substrate have excellent performance due to advantages such as a high quality factor, Q, low loss insertion, large bandwidth, etc. Prior to manufacturing, a comprehensive analysis and proper design are essential to evaluating the device’s key performance indicators, including the Bode Q value, bandwidth, and transverse mode suppression. This study explored the performance of SAW resonators employing a 42°Y-X LiTaO3 (LT) thin-plate-based multi-layered piezoelectric substrate. The thicknesses for each layer of the 42°Y-X LT/SiO2/poly-Si/Si substrate were optimized according to the index of phase velocity, Bode Q value, and bandwidth. The effect of the device structure parameters on the dispersion curve and slowness curve was studied, and a flat slowness curve was found to be favorable for transverse mode suppression. In addition, the design of the dummy configuration was also optimized for the suppression of spurious waves. Based on the optimized design, a one-port resonator on the 42°Y-X LT/SiO2/poly-Si/Si substrate was fabricated. The simulation results and measurements are presented and compared, which provides guidelines for the design of new types of SAW devices configured with complex structures.