To improve crop model performance for regional crop yield estimates, a new four-dimensional variational algorithm (POD4DVar) merging the Monte Carlo and proper orthogonal decomposition techniques was introduced to develop a data assimilation strategy using the Crop Environment Resource Synthesis (CERES)-Wheat model. Two winter wheat yield estimation procedures were conducted on a field plot and regional scale to test the feasibility and potential of the POD4DVar-based strategy. Winter wheat yield forecasts for the field plots showed a coefficient of determination (R2) of 0.73, a root mean square error (RMSE) of 319 kg/ha, and a relative error (RE) of 3.49%. An acceptable yield at the regional scale was estimated with an R2 of 0.997, RMSE of 7346 tons, and RE of 3.81%. The POD4DVar-based strategy was more accurate and efficient than the EnKF-based strategy. In addition to crop yield, other critical crop variables such as the biomass, harvest index, evapotranspiration, and soil organic carbon may also be estimated. The present study thus introduces a promising approach for operationally monitoring regional crop growth and predicting yield. Successful application of this assimilation model at regional scales must focus on uncertainties derived from the crop model, model inputs, data assimilation algorithm, and assimilated observations.