Recently, module-integrated converter (MIC) research has shown interest in small-scale photovoltaic (PV) generation. The converter is capable of efficient power generation. In this system, the high frequency transformer should be made compact, and demonstrate high efficiency characteristics. This paper presents a core structure optimization procedure to improve the efficiency of a high frequency transformer of compact size. The converter circuit is considered in the finite element analysis (FEA) model, in order to obtain an accurate FEA result. The results are verified by the testing of prototypes.