The study of reservoir storage capacity can provide a valuable guide to the rational protection and utilization of water resources. With regard to the current situation and shortcomings of the estimation of reservoir storage, the remotely measured water levels of a reservoir are extracted by a Radar Altimeter (RA), and the surface water area is collected with a Multi-Spectral Instrument (MSI) and a Synthetic Aperture Radar (SAR). Then a reservoir storage estimation model based on data assimilation of multi-source remote sensing is established. Finally, a reservoir storage estimation system based on multi-source remote sensing data is developed, which can obtain remotely measured water levels and water area and estimate water storage capacity without contact. Experimental results prove that this system has stability and versatility. It is expected to be applied to flood control, drought resistance, reservoir dispatching and other fields to provide a technical support for the scientific and efficient management of reservoirs