Recently, the module-integrated converter has shown an interest in the photovoltaic generation system. In this system, the high frequency transformer should be compact and efficient. The proposed method is based on the correlation characteristic between the copper and core loss to minimize the loss of transformer. By sizing an effective cross-sectional area and window area of core, the amount of loss is minimized. This paper presents the design and analysis of high frequency transformer by using the 3D finite element model coupled with DC-DC converter circuit for more accurate analysis by considering the nonlinear voltage and current waveforms in converter circuit. The current waveform in each winding is realized by using the ideal DC voltage source and switching component. And, the thermal analysis is performed to satisfy the electrical and thermal design criteria.