This work is devoted to the first analysis of temperature fields related to chemical microfluidic reactors. The heat transport around and inside a microchannel is both convective and diffusive with spatial distribution of source terms and strong conductive effects in the channel surrounding. With simplified assumptions, it is shown that Infrared thermography and processing methods of the temperature frames allow to estimate important fields for the chemical engineers, such as the heating source distribution of the chemical reaction along the channel. A validation experiment of a temperature field processing method is proposed with Joule effect as calibrated source term and non reactive fluids. From such previous experiment, a Peclet field is estimated and used in a further step in order to study an acid-base flow configuration.