The use of satellite-based passive microwave brightness temperatures (TBs) is an effective way to retrieve the cloud water content (CWC) of broad cloud systems, but it is challenging to estimate CWC over land due to complexities of cloud processes and uncertainties in strong and heterogeneous land emissions. We proposed a method to estimate CWC over land at multiple-kilometer resolutions and to concurrently assimilate the estimated CWC into the model by using multi-frequency TBs and coupled land and atmosphere assimilation. The estimated CWC was in good accordance with vertical two-dimensional products of CloudSat in terms of cloud water path (CWP) and the vertical distribution of CWC. In addition, we examined the uncertainties of this method by sensitivity analysis of CWC estimates of TBs and cloud top height. The results suggested that the error in TBs is not large, and that cloud top height affects the estimated CWC more sensitively than TBs. The addition of cloud top height information from other satellite observations as a constraint of optimization allows further improvement of the vertical distributions of CWC. This study revealed that the proposed method has great potential to provide unprecedented data for CWC with adequate accuracy, which are continuously distributed over land and ocean.