Provided is a biochemical analyzer in which a microfluidic biochemical assay may be performed. The analyzer includes: a microfluidic device loading space including a microfluidic device supporting unit detachably supporting a microfluidic device including an energy application region in which an energy is applied; an energy source loading space including an energy source applying the energy to the 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 window through which the energy can be transmitted. A method of controlling an internal temperature of the biochemical analyzer is also provided.