The invention discloses a method for reducing grounding resistance in manner of digging a grounding deep well in a transformer station, comprising steps of calculating a station address soil layered model, calculating target parameters like a power frequency grounding resistance safety value of a horizontal grounding grid and safety values of a contact potential difference and a step potential difference, obtaining a power frequency grounding resistance calculation value of a horizontal grounding grid and calculation values of the contact potential difference and the step potential difference, determining the amount, the positions, the well depth, the perpendicular grounding electrode materials and equivalent radiuses of the grounding deep wells, regulating the parameters of the grounding deep well, providing a horizontal grounding grid material table, a perpendicular grounding body material table, rise of earth potential, the power frequency grounding resistance, the calculation values and the safety values of the contact potential difference and the step potential difference of the grounding grid of the station. The invention can dramatically reduce the grounding resistance of the transformer station, enables the contact potential difference and the step potential difference to be reduced to below the safety value, and enables the design of the high soil resistivity and transformer station grounding system having the ground water layer to be simple, accurate and effective.