The purpose of this work was to develop a non-contact characterization technique based on infrared thermography (IRT) for millifluidics reactors dedicated to exo or endothermal chemical reactions. An acid (HCl)-base (NaOH) reaction was performed using concentric injection of the reactants. Droplets of small volume (μL) were generated and were carried downstream by inert oil in TEFLON tubing. A color indicator was added to enable monitoring of the reaction evolution by visible imaging. Thus, coupled IRT and visible imaging are used to characterize the reaction. From the IRT temperature fields, a thermal evaluation enables estimation of the enthalpy with less than 2% error. In addition, characterization of the kinetics and the mixing dynamics was performed by both techniques. It was shown through a quantitative relation that the kinetics and mixing dynamics are predicted with 90% precision. In addition, the dynamics inside the droplets can be represented as a diffusion phenomenon, where species are carried inside with an apparent diffusion coefficient that is more than 10 times the molecular coefficient 3 × 10−9 m s−1. Moreover, the mixing time of millifluidic droplets for a given channel (i.e., fixed inner diameter) is influenced by the droplet length and velocity. In contrast, there is no influence of the droplet length on the apparent diffusion coefficient for a given constant velocity. Finally, it was shown through characterization of the diode reaction that this novel non-intrusive technique based on millifluidic and IRT is a convenient and powerful tool for the characterization of biphasic flows, highly exothermic chemical reactions and other physical phenomena such as phase changes.