Multilayer separate polymer injection in concentric dual-tubing is a special method for enhancing oil recovery in later development stage of the multilayer formation. During the injection process, heat exchange occurs among the inner tubing, tubing annulus and formation, making the thermal transfer process more complicated than traditional one. This work focuses on the polymer flowing characteristics during the multilayer separate polymer flooding injection process in the wellbore. A temperature–viscosity numerical model is derived to investigate the influencing factors on polymer dual-tubing injection process. Then, an estimate-correct method is introduced to derive the numerical solutions. Several influences have been discussed, including the axial temperature distribution, viscosity distribution, pressure drop, and flow pattern of polymer. Results show that under low injecting rates, below 5 m3/d, formation temperature will greatly decrease the polymer viscosity. When the injecting rates above 20 m3/d, the polymer just decreases 1–3 mPa·s at the bottom of well, which is really small. Additionally, the temperature distribution, the coefficient of friction under different injecting rates have been discussed. Generally, this method provides a new way to analyze thermal conductivity during the polymer injection process which is meaningful for polymer flooding in the oilfield application.