Polymer flooding (PF) in heterogeneous heavy oil reservoirs is not only closely related to polymer degradation, but also to non-Newtonian flow. In this paper, both experimental and simulation methods are combined to investigate this type of flooding. Through experiments, the degradation of polymer, rheological properties of fluids, and flow of fluids in porous media were determined. Based on the experimental results, a novel mathematical model was established, and a new PF simulator was designed, validated, and further applied to study the effects of polymer degradation, polymer solution shear thinning, and non-Newtonian flow on PF in heterogeneous heavy oil reservoirs. These experimental results demonstrated that the polymer first-order static degradation rate constant was lower than the polymer first-order dynamic degradation rate constant; the polymer solution and heavy oil were non-Newtonian fluids, with shear thinning and Bingham fluid properties, respectively; and the heavy oil threshold pressure gradient (TPG) in low-permeability porous media was higher than that in high-permeability porous media. All comparison results showed that the designed simulator was highly accurate and reliable, and could well describe both polymer degradation and non-Newtonian flow, with special emphasis on the distinction between polymer static and dynamic degradation and heavy oil TPG. Furthermore, the simulation results verified that polymer degradation, polymer solution shear thinning, and heavy oil TPG all had negative effects on the efficiency of PF in heterogeneous heavy oil reservoirs.