The Three Gorges reservoir is the typical channel type reservoir in the Changjiang River, China. The dynamic storage can better reflect the true situation of water storage, so it's one of the important parameters of the water balance's calculation, runoff forecast and reservoir operation for a channel reservoir. Combining the GIS technology with the hydrodynamic method, this paper proposed a rapid and accurate computation method of the channel type reservoirs'dynamic storage. And the method has been successfully applied to the Three Gorges Reservoir real-time operation. As the reservoir topographic DEM data is usually a great data mass and redundancy, the block-based processing, run-length encoding raster data compression method and multi-bands integration method were employed to manage the parameters. The efficiency of the spatial interpolation method's computation has been evidently improved and the rapid computation of the dynamic storage has been realized. On the basis of the method, a software system of reservoir storage calculation was developed and used to calculate the dynamic storage of the Three Gorges Reservoir. The calculation speed is very quick and the calculated result errors are very small, which indicates that the method is valid and feasible.