The paper presents a novel reduced order model which enables the heat transfer analysis of microchannels consisting of continuously moving microdroplets with constant heat flux on the wall. Due to the low Reynolds number which is typical in microfluidic applications, the hydrodynamics can be described as Taylor-flow. Two-phase Taylor-flow is the basis of many microfluidic applications such as bio-chemical microreactors where segmented zones are required to accurately characterize enzyme reactions. This new model represents a microtube with horizontally alternating and moving phases. The results obtained by the reduced order model match the results of a validated detailed Ansys-Fluent model with 5 % accuracy at the channel wall. The reduced order model accounts for microcirculation and back flow. The proposed reduced order model of the two-phase Taylor-flow is foreseen to be included in system level description of chemical microrectors.