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The computational study of transient immiscible and incompressible two-phase flows is one of the most common and desirable way for investigation of engineering phenomena and physics science. In the previous studies, generally bubbles current have been used as an active method for increasing heat transfer, however, due to existence of hydraulic boundary layers, the bubbles were not able to cross over this layer to thinning the thermal boundary layer and consequently the efficiency of this method was not very considerable. In this study, by considering potential of magnetic field, the effect of co-applying of external non uniform magnetic field and magnetic bubbles in enhancing the heat transfer efficiency in a 3-D tube has been investigated. The computational model consisted of the Navier–Stokes equation for liquid phase and VOF model for interface tracking are carried out by OpenFOAM. The external magnetic field has been considered non-uniform and time dependent. The results predicted that magnetic bubbles and external magnetic field due to their effect on thermal boundary layer increased significantly heat transfer and Nusselt number. Furthermore, results indicated magnetic bubbles can act as an active torbulators in the flow field and can be applied for increasing recirculation and secondary flow in the flow field. The average temperature and magnetic field over times for different cases have been discussed in the results.