The invention provides a calculating method for initial oil saturation in a water flooded layer of a core drilling well during a high water cut period. The method comprises observing construction of oil deposit and reservoir geological condition, collecting effective porosity of an oil layer of the core drilling well under the initial condition as well as initial oil saturation data of coring analyses; taking oil and water saturation data on routine analyses of rock samples as a base and obtaining underground oil and water saturation; utilizing effective porosity after compressed and correction and oil saturability after degassed correction, taking sand-parting layer groups, sand-parting segments or oil-separating groups to respectively create regression equations; clarifying the sub-well scanning rule and determining pairs of sub-wells in the initial conditions corresponding to all layer sections of the enclosed core drilling well during a high water cut period; solving the initial physical parameters during a high water cut period; and taking sand-separating layer groups of restored physical reservoir parameters to the regression equations such that initial saturation during the water cut period can be solved. The calculating method for initial oil saturation in the water flooded layer of the core drilling well during the high water cut period has following beneficial effects: big calculating errors are avoided in the conventional method for solving initial oil saturation in the water flooded layer of the core drilling well during the high water cut period.