A mixing device composed of a micron scale flow channel was applied as a continuous reactor to control exothermic reaction heat and to increase the product yield, in a synthesis of a pharmaceutical intermediate of quinolone antibiotics. The model reaction featured a fast reaction rate, high heat generation, and impurity formation due to a prolonged contact time between reactants and products. Using the micromixer reactor, the reaction heat was efficiently removed so that virtually no impurities were produced during the reaction. A product yield comparable to the theoretical value was achieved in a single micromixer unit. Optimum operating conditions were acquired from a statistical method by using factorial design, which was also verified by a CFD calculation.