The DC high voltage power supply is used to power the Accelerator-Based Boron Neutron Capture Therapy (AB-BNCT) device, and its output DC high voltage greatly affects the performance of AB-BNCT device. As the core device of DC high voltage power supply, the high frequency and high voltage transformer undertakes the important task of boosting voltage. In this paper, the design process of high frequency and high voltage transformer is analyzed from three aspects: distribution parameter optimization, hollow structure design and winding structure design. The leakage inductance and distributed capacitance produced by different coil structures are calculated theoretically, and the transformer distribution parameters are optimized through Z-shaped connection. The design scheme of the hollow structure is determined by analyzing the electromagnetic characteristics of various magnetic core materials. The loss of winding coils with different structures is analyzed by using AC resistance coefficient, and the multi-layer Litz wire is determined as the winding conductor. The coupling degree and energy storage between winding coils with different structures are characterized by inductance value, and the coil structure of the transformer is determined to be a ring structure. Finally, the electromagnetic characteristics of high frequency and high voltage transformer are analyzed by finite element method, and the reliability of the design scheme of high frequency and high voltage transformer is verified.