The ensemble Kalman smoother (EnKS) is introduced to the data assimilation system, ASTI, based on the integrated transport simulation code, TASK3D. We use the EnKS to estimate state variables composed of electron and ion temperature, density, and numerical factors of turbulent transport models and neutral beam injection (NBI) heat deposition. The time series data of plasma temperature and density profiles are assimilated into TASK3D. The estimation performance of the EnKS is investigated, and the EnKS is applied to an NBI plasma in the Large Helical Device (LHD) (shot:114053) to estimate the factors of the turbulent heat transport model. The obtained factors can reproduce the experimental temperature data with high accuracy. These results indicate the effectiveness and validity of the EnKS approach for accurate estimation of fusion plasma parameters.