Surface acoustic wave (SAW) strain sensors fabricated on piezoelectric substrates have attracted considerable attention due to their attractive features such as passive wireless sensing ability, simple signal processing, high sensitivity, compact size and robustness. To meet the needs of various functioning situations, it is desirable to identify the factors that affect the performance of the SAW devices. In this work, we perform a simulation study on Rayleigh surface acoustic wave (RSAW) based on a stacked Al/LiNbO3 system. A SAW strain sensor with a dual-port resonator was modeled using multiphysics finite element model (FEM) method. While FEM has been widely used for numerical calculations of SAW devices, most of the simulation works mainly focus on SAW modes, SAW propagation characteristics and electromechanical coupling coefficients. Herein, we propose a systematic scheme via analyzing the structural parameters of SAW resonators. Evolution of RSAW eigenfrequency, insertion loss (IL), quality factor (Q) and strain transfer rate with different structural parameters are elaborated by FEM simulations. Compared with the reported experimental results, the relative errors of RSAW eigenfrequency and IL are about 3% and 16.3%, respectively, and the absolute errors are 5.8 MHz and 1.63 dB (the corresponding Vout/Vin is only 6.6%). After structural optimization, the obtained resonator Q increases by 15%, IL decreases by 34.6% and the strain transfer rate increases by 2.4%. This work provides a systematic and reliable solution for the structural optimization of dual-port SAW resonators.