As a key variable in the surface hydrological cycle and energy balance, soil moisture is often analyzed using data assimilation to improve precise and high spatiotemporal resolution from multisource data. However, accurate estimation of model error in soil moisture data assimilation is not sufficient in spatial and temporal dimensions. This paper proposes a spatiotemporal error estimation method that integrates the spatial and temporal dimensions of the study area into model error estimation. The in-situ data was regarded as the “true value” for the temporal dimensions model error estimation. The triple collocation (TC) technique was used to estimate the spatial error of the model. Based on the aforementioned estimation, a linear method to construct the relationship between spatial and temporal information was proposed to fuse the spatiotemporal model error. Result from the proposed method was compared against the overall model error estimation and spatial estimation methods in ensemble Kalman filter (EnKF) data assimilation. The ERA-Interim reanalysis data and in-situ soil moisture data from Washington State in 2016 were used to evaluate the performance of EnKF data assimilation. Using statistical metrics, including the root mean square error (RMSE), the mean bias error (MBE), and the Pearson correlation coefficient (i.e., R-value), the results show that our proposed approach, which uses spatiotemporal approach to model error estimation in EnKF data assimilation, yielded more accurate soil moisture estimates. When ERA-Interim reanalysis soil moisture data was used as the reference data, compared with the overall model error estimation EnKF Data Assimilation Experiment, RMSE and MBE of spatiotemporal model error estimation EnKF Data Assimilation Experiment were reduced by 0.0062 and 0.0061 m³ / m³, respectively, and R remained basically unchanged. When using in-situ measurements as reference data, RMSE and MBE decreased by 0.0034 and 0.0038 m³ / m³, respectively, and R increased by 0.0365. Compared with the other estimation approaches in the experiments, the spatiotemporal error estimation approach greatly improved the estimation accuracy of soil moisture analysis, yielding the closest values and variation trends with the in-situ measurements. Fully considering the temporal and spatial variation of model error and improving the estimation accuracy of model error can provide more accurate model information for data assimilation. The proposed method and framework in this paper can be used in model error estimation and data assimilation, particularly in the fields of numerical weather forecasting, natural environment monitoring, and geographical environment research.