History matching is essential for estimating reservoir performances and decision makings. Ensemble Kalman filter (EnKF) has been researched for inverse modeling due to lots of advantages such as uncertainty quantification, real-time updating, and easy coupling with any forward simulator. However, it requires lots of forward simulations due to recursive update. Although ensemble smoother (ES) is much faster than EnKF, it is more vulnerable to overshooting and filter divergence problems. In this research, ES is coupled with both clustered covariance and selective measurement data to manage the two typical problems mentioned. As preprocessing work of clustered covariance, reservoir models are grouped by the distance-based method, which consists of Minkowski distance, multidimensional scaling, and K-means clustering. Also, meaningless measurement data are excluded from assimilation such as shut-in bottomhole pressures, which are too similar on every well. For a benchmark model, PUNQ-S3, a standard ES with 100 ensembles, shows severe over- and undershooting problem with log-permeability values from 36.5 to −17.3. The concept of the selective use of observed data partially mitigates the problem, but it cannot match the true production. However, the proposed method, ES with clustered covariance and selective measurement data together, manages the overshooting problem and follows histogram of the permeability in the reference field. Uncertainty quantifications on future field productions give reliable prediction, containing the true performances. Therefore, this research extends the applicatory of ES to 3D reservoirs by improving reliability issues.