Soil moisture plays an important role in climate prediction and drought monitoring. Data assimilation, as a method of integrating multi-geographic spatial data, plays an increasingly important role in estimating soil moisture. Model prediction error, an important part of the background field information, occupies a position that could not be ignored in data assimilation. The model prediction error in data assimilation consists of three parts: forcing data error, initial field error, and model error. However, the influence of model error in current data assimilation methods has not been completely considered in many studies. Therefore, we proposed a theoretical framework of the ensemble Kalman filter (EnKF) data assimilation based on the breeding of growing modes (BGM) method. This framework used the BGM method to perturb the initial field error term w of EnKF, and the EnKF data assimilation to assimilate the data to obtain the soil moisture analysis value. The feasibility and superiority of the proposed framework were verified, taking into consideration breeding length and ensemble size through experiments. We conducted experiments and evaluated the accuracy of the BGM and the Monte Carlo (MC) methods. The experiment showed that the BGM method could improve the estimation accuracy of the assimilated soil moisture and solve the problem of model error which is not fully expressed in data assimilation. This study can be widely used in data assimilation and has a significant role in weather forecast and drought monitoring.