Provided is a biochemical analyzer including: a microfluidic device loading space including a microfluidic device supporting unit detachably supporting a microfluidic device including an electromagnetic radiation application region in which electromagnetic energy is applied; an energy source loading space including an energy source applying the electromagnetic energy to the electromagnetic radiation application region; and an isolation wall isolating the microfluidic device loading space and the energy source loading space to prevent heat transfer between the microfluidic device loading space and the energy source loading space and including a transparent window through which the electromagnetic energy can be transmitted. A method of controlling an internal temperature of the biochemical analyzer is also provided.