This article has shown the design and characterization of silicon-integrated thin-film micro-transformers and their application in a quasi-resonant flyback converter. Two micro-transformers with different turn ratios of 4:4 and 3:3 were designed. The micro-transformers in this study have elongated spiral shape windings sandwiched between two layers of the thin-film magnetic core, and this structure can leverage the anisotropic core property. The micro-transformers were built on a silicon substrate using micro-electro-mechanical systems (MEMSs) fabrication process to ensure a high integration level and high power density. The inductance of 4:4 and 3:3 micro-transformers are 57.3 and 31.5 nH, respectively, their coupling coefficients are 90.5% and 82.7% at 30–40 MHz, and the measured quality factors are 7.82 at 21 MHz and 8.94 at 35 MHz, respectively. A resonant flyback converter topology deploying with a high electron mobility transistor [Gallium nitride (GaN)] was used to evaluate the electrical performance of two micro-transformers. Two resonant flyback converters operating at zero voltage switching (ZVS) reached the maximum conversion efficiency of 46.4% (3:3) and 45.7% (4:4), respectively, with 3.3 V input. The 3:3 micro-transformer developed in this work achieved the highest power density of 128 mW/mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> with a similar efficiency compared to other cored micro-transformers. The loss analysis of the flyback conversion circuit shows that the main losses in the circuit are the copper winding loss of the micro-transformer and the eddy current loss of the magnetic core. The conversion efficiency of the circuit will be improved by applying thicker copper and core lamination in the future.