Microchannel tube (MCT) is widely employed in industry due to its excellent efficiency in heat transfer. An MCT is commonly produced through extrusion within a porthole die, where severe plastic deformation is inevitably involved. Moreover, the plastic deformation, which dramatically affects the final property of the MCT, varies significantly from location to location. In order to understand the development of the microstructure and its effect on the final property of the MCT, the viscoplastic self-consistent (VPSC) model, together with the finite element analysis and the flow line model, is employed in the current study. The flow line model is used to reproduce the local velocity gradient within the complex porthole die, while VPSC model is employed to predict the evolution of the microstructure accordingly. In addition, electron backscatter diffraction (EBSD) measurement and mechanical tests are used to characterize the evolution of the microstructure and the property of the MCT. The simulation results agree well with the corresponding experimental ones. The influence of the material’s flow line on the evolution of the orientation and morphology of the grains, and the property of the produced MCT are discussed in detail.