Owing to the increasing demand for low-power electronic devices, the need for miniaturized, light-weight power supplies with a high power density is growing. A piezoelectric transformer, which is a mechanical resonance-based power transformer, can meet these requirements. However, piezoelectric transformers are based on mechanical resonance, and the resonance characteristics depend on the output current, temperature, and other parameters. Thus, their efficiency may rapidly reduce with changes in the resonance characteristics under specific load and temperature conditions. Therefore, this study proposes a technique that estimating the optimal frequency by using the measurements of the input voltage and current phase difference of the piezoelectric transformer and regulating the output voltage using the duty cycle. Modeling and control system analyses are performed to address the control interference problem caused by the plurality of control variables and control outputs. To demonstrate the proposed technique, a 40 W prototype hardware device is developed. The efficiency improvement is confirmed, and the analysis is validated.