The aim of this paper is to propose a new thermal method devoted to the estimation of heat exchange coefficients in isoperibolic biphasic millifluidics devices. First, an experimental set up, which couples InfraRed and visible measurements of the droplets flow is presented. Then, a Lagrangian approach is apply to work in the space of each biphasic plug (by using visible measurements) in order to demonstrate that a simple two temperatures (given by IR measurements) thin body thermal model is enough consistent to represent the thermal behaviour of such complex and heterogeneous millifluidic configuration. By using an inverse processing method, it is shown that the estimation of the heat transfer coefficients is quite easy and accurate for several flow rate ratio of the two phases. Finally, a first correlation allowing the calculation of the heat exchange coefficients by the knowledge of the thermal properties and the flow rate ratio of each phase is presented.