The paper presents a reduced order thermal model, which enables the thermal analysis of two-phase 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 is represent 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 in system level description of chemical microrectors.Index Terms-Compact thermal modeling, segmented slug flow, Lab-on-a-Chip, calorimetry Nomenclature A Bubble Cross-sectional area of the bubble [m 2 ] c V Volumetric specific heat capacity [J/m 3 K] Ca Capillary number δ F Fluid film thickness [m] λ Thermal conductivity [W/m · K] L 1 L 2 First and second part of the cylindrical Laplace matriẋ q Heat generation rate [W/m 3 ] q Heat flux [W/m 2 ] r Radius [m] Re Reynolds number res Resolution of the model [m] ρ Density [kg/m 3 ] T Temperature [K] ∆T Avg Average temperature rise on wall [K] t Time [s] v Average velocity [m/s] V Volume [m 3 ]