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We proposed a temperature-controlled miniaturized cell for use in a magnetic beads handling system for bio-chemical reaction, especially for PCR usage, and created it by using conventional high-precision processing technologies. The proposed system consists of four temperature-controlled cells (designed for PCR use), a flow channel, a permanent magnet, and a compact linear actuator for driving the magnet. We introduced a miniaturized metallic armor and covered the cell unit with it to increase the liquid temperature uniformity in a cell. We experimentally evaluated the temperature distribution of the system by using thermography, and obtained a temperature distribution in the center (3.5 times 3.5 mm) that was less than 1.0degC.