A high-overtone bulk acoustic resonator (HBAR) consisting of a piezoelectric film with two electrodes on a substrate exhibits a high quality factor (Q) and multi-mode resonance spectrum. By analyzing the influences of each layer’s material and structure (thickness) parameters on the effective electromechanical coupling coefficient (Keff2), the resonance spectrum characteristics of Keff2 have been investigated systematically, and the optimal design of HBAR has been provided. Besides, a device, corresponding to one of the theoretical cases studied, is fabricated and evaluated. The experimental results are basically consistent with the theoretical results. Finally, the effects of Keff2 on the function of the crystal oscillators constructed with HBARs are proposed. The crystal oscillators can operate in more modes and have a larger frequency hopping bandwidth by using the HBARs with a larger Keff2·Q.