Metformin is a drug for type 2 diabetes used as the first-line mainly in North America and Europe. Its mechanism of action is believed to lower blood glucose levels by inhibiting gluconeogenesis in the liver and increasing glucose consumption in peripheral tissues. However, there are still controversies regarding the target molecules and the biochemical networks that induce pharmacological actions downstream of the target molecules. We applied the methodology of trans-omics analysis, which elucidates metabolic regulatory mechanisms as a large-scale molecular network, to characterizing the mechanism of action of metformin in the liver. We will show comprehensive identification of target proteins and reconstruction of metabolic regulatory networks that induce pharmacological actions of metformin.