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Carbon Capture and Storage (CCS) is one of the effective means to reduce the carbon dioxide concentration in atmosphere. Deep saline aquifer is the most potential storage sites because of its wide spread and the huge storage capacity. The storage capacity of deep saline aquifer was determined by hydrogeological parameters of the assessed aquifer. Spatial discretization method based on the geostatistical method takes account of the spatial variability of hydrogeological parameters involved in capacity assessment, which applied by inputting the value of hydrological parameters of every cell and calculating the storage capacity of each cell. The total storage capacity in assessed area was the summation of all cells. In the Central Depression of Songliao Basin, the theoretical carbon dioxide storage capacity of deep saline aquifers was estimated as 81.80Gt with spatial discretization method. Compared with the other methods, this method can reflect the spatial characteristics of the carbon dioxide storage capacities and was more precise.