Ionospheric total electron content (TEC) is important data for ionospheric morphology, and also an important parameter for ionospheric correction in Global Navigation Satellite System (GNSS) precise positioning, navigation, and radio science. In this study, we present a data assimilation model for regional ionosphere based on a local ensemble Kalman filter (LEnKF) with the International Reference Ionosphere 2016 (IRI-2016) model as the background, to assimilate ionospheric TEC observations from GNSS. To demonstrate the results, the TEC estimates from the Crustal Movement Observation Network of China (CMONOC), which is about 260 stations in China, are applied as observation. The assessments are performed against the TEC estimates from BeiDou Navigation Satellite System (BDS) geostationary earth orbit (GEO) and against the final products from the Center for Orbit Determination in Europe (CODE). The assimilation results are in good agreement with BDS GEO TEC and the CODE TEC on a quiet or disturbed day. The correlation coefficient after assimilation is increased by about 17% compared with that before assimilation, and the RMSE after assimilation is decreased by about 42% compared with that before assimilation. Furthermore, the assimilated method is also evaluated in the single-frequency precise point positioning (PPP). The experimental results indicate that the PPP/Assimilated method can improve the GNSS positioning accuracy more effectively in comparison to the PPP/CODE. These results reveal that the LEnKF method can be considered as a useful tool for ionospheric assimilation.