A SAW device with a multi-layered piezoelectric substrate has excellent performance due to its high Q value. A multi-layer piezoelectric substrate combined with phononic crystal structures capable of acoustic wave reflection with a very small array can achieve miniaturization and high performance. In this paper, a honeycomb-shaped phononic crystal structure based on 42°Y-X LT/SiO2/poly-Si/Si-layered substrate is proposed. The analysis of the bandgap distribution under various filling fractions was carried out using dispersion and transmission characteristics. In order to study the application of PnCs in SAW devices, one-port resonators with different reflectors were compared and analyzed. Based on the frequency response curves and Bode-Q value curves, it was found that when the HC-PnC structure is used as a reflector, it can not only improve the transmission loss of the resonator but also reduce the size of the device.