This study introduces a new scale-dependent viscosity model, in which transesterification reaction of polycarbonate/poly(ethylene terephthalate) (PC/PET) blends with various phase morphologies and micro-scale effects have been taken into account. It is found that a Power-law model can be used to quantitatively describe the relationship between the degree of transesterification and shear rate employed during compounding of PC and PET. A micro-scale viscosity model, which incorporates the micro-scale effects, has been developed by characterizing the flow using a double-barrel capillary rheometer with different microscale channels. For both neat PC and PC/PET blends, under the conditions of the constant shear rate and melt temperature, the shear viscosity dropped with decreasing capillary diameter because of the wall-slip effect. The proposed viscosity model based on the Cross equation can describe the variation of shear viscosity for PC/PET blends under both macro- and micro-scale conditions. Less than 7% average error is obtained between the model predictions and rheological experimental data. Filling simulation and micro-injection molding (μIM) short-shot experiments were conducted to validate the accuracy of the proposed viscosity model. For all the L9(34 ) design of experiment (DOE) molding trials, the average relative error under the micro-scale condition was 4.5±1.1%, which is much smaller than that of the average relative error under the macro-scale condition at 11.4±2.7%.