To accurately estimate winter wheat yields and analyze the uncertainty in crop model data assimilations,winter wheat yield estimates were obtained by assimilating measured or remotely sensed leaf area index(LAI) values. The performances of the calibrated crop environment resource synthesis for wheat(CERES-Wheat) model for two different assimilation scenarios were compared by employing ensemble Kalman filter(EnKF)-based strategies. The uncertainty factors of the crop model data assimilation was analyzed by considering the observation errors,assimilation stages and temporal-spatial scales. Overall,the results indicated a better yield estimate performance when the EnKF-based strategy was used to comprehensively consider several factors in the initial conditions and observations. When using this strategy,an adjusted coefficients of determination(R~2) of 0.84,a root mean square error(RMSE) of 323 kg ha~(–1),and a relative errors(RE) of 4.15% were obtained at the field plot scale and an R~2 of 0.81,an RMSE of 362 kg ha~(–1),and an RE of 4.52% were obtained at the pixel scale of 30 m×30 m. With increasing observation errors,the accuracy of the yield estimates obviously decreased,but an acceptable estimate was observed when the observation errors were within 20%. Winter wheat yield estimates could be improved significantly by assimilating observations from the middle to the end of the crop growing seasons. With decreasing assimilation frequency and pixel resolution,the accuracy of the crop yield estimates decreased; however,the computation time decreased. It is important to consider reasonable temporal-spatial scales and assimilation stages to obtain tradeoffs between accuracy and computation time,especially in operational systems used for regional crop yield estimates. To accurately estimate winter wheat yields and analyze the uncertainty in crop model data assimilations, winter wheat yield estimates were obtained by assimilating measured or remotely sensed leaf area index (LAI) values. The performances of the calibrated crop environment resource for wheat (CERES- The uncertainty factors of the crop model data assimilation was calculated by considering the observation errors, assimilation stages and temporal-spatial scales. Overall, the results indicated a better yield estimate performance when the EnKF-based strategy was used to comprehensively consider several factors in the initial conditions and observations. When using this strategy, an adjusted coefficients of determination (R ~ 2) of 0.84, a root mean square error (RMSE) of 323 kg ha -1, and a relative errors (RE) of 4.15% were obtained at the field plot scale and an R ~ 2 of 0.81, an RMSE of 362 kg ha ~ (-1), and an RE of 4.52% were obtained at the pixel scale of 30 m × 30 m. With increasing observation errors, the accuracy of the yield estimates obviously decreased, but an acceptable estimate was observed when the observation errors were within 20%. Winter wheat yield estimates could be improved significantly by assimilating observations from the middle to the crop of the growing seasons. With decreasing assimilation frequency and pixel resolution, the accuracy of the crop It is important to consider reasonable temporal-spatial scales and assimilation stages to obtain tradeoffs between accuracy and computation time, especially in operational systems used for regional crop yield estimates.