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Microwave backscattering models play key roles in surface scattering modeling and soil moisture inversion in active microwave remote sensing. However, numerous evaluations indicate that significant discrepancies between the model simulations and radar observations remain, and these discrepancies are regarded to be attributed to inaccuracies in the models. What do such discrepancies originate from is unclear and has not been comprehensively analyzed. To this end, this paper presents an uncertainty analysis to explore the intrinsic reason for the discrepancies between the backscattering model simulations and radar observations. The probability distribution function and the corresponding statistical characteristics are introduced to describe the uncertainty in the model outputs. We find that the scale dependence of the key model inputs leads to significant uncertainties in the model inputs, and the uncertainties are transferred into the model outputs. Thus, the discrepancies between the model simulations and radar observations are intrinsically caused by the spatial scaling and related uncertainties of key model inputs. In short, the scale mismatch between the model inputs and remote sensing pixels is an intrinsic factor that causes the discrepancies between the model simulations and radar observations. This finding suggests that the scaling effect of model inputs should be carefully considered when using the backscattering models at the pixel scale, and equivalent inputs matched at the corresponding scales should be developed for remote sensing applications. Thus, this analysis insights into the scale dependence of inputs for backscattering models and suggests to provide scale-matched inputs where the models are applied at different scales.