The temperature dependence of the viscosity of starch-filled poly(hydroxy ester ether) (PHEE) biodegradable composites was analyzed using Arrhenius and WLF equations. Corn starch/PHEE materials were extruded using a twin screw extruder with starch volume fractions from 0.27 to 0.66. Dynamic strain sweep measurements were carried out at 10 rad/s at six different temperatures from 100 °C to 150 °C. Both Arrhenius and WLF equations model equally well the temperature effect on viscosity of PHEE and starch/PHEE composites with starch volume fractions up to 0.36. Arrhenius equation with stress correction describes the stress dependence of viscosity of starch/PHEE composites with higher starch volume fractions. The activation energy using both Arrhenius equation and Arrhenius equation with stress correction is 62.7 kJ/mol for pure PHEE and starch/PHEE composites.