This paper presents a new design of silicon-based biocalorimeter made with dual thermopiles and a microfluidic channel introducing a splitting and mixing flow. The dualthermopile was fabricated with chromium and copper using microelectromechanical system (MEMS) technique, and the microfluidic channel was made of PDMS using a soft-lithography. Each thermopile consists of 26 Cr/Cu thermocouple pairs. The sensitivity of each thermocouple is 20.0 μCV/K and the total sensitivity of thermopile is 519.2 μV/K. This dual-thermopile system enables biocalorimeter to acquire the reliable data in a rapid and convenient manner because it detects biochemical reaction and reference temperature simultaneously.