The invention relates to an electrified railway technology, in particular to a subsurface tunnel waterstop structure used for protecting a groundwater environment and a construction method thereof. The waterstop structure comprises a plurality of vertical frozen earth waterstop layers distributed sequentially in the tunnel direction and horizontal waterstop layers surrounding the outer contour of a tunnel, and the horizontal waterstop layers extend in the extending direction of the tunnel; the vertical frozen earth waterstop layers and the horizontal frozen earth waterstop layers intersect with each other; and the bottoms of the vertical frozen earth waterstop layers are lower than the bottoms of the horizontal frozen earth waterstop layers; and tunnel lining structures are arranged between the horizontal frozen earth waterstop layers and the tunnel. The vertical frozen earth waterstop layers and the horizontal frozen earth waterstop layers are adopted to form a cup-shaped frozen earth waterstop layer, the groundwater environment is protected, and groundwater is prevented from being polluted in the tunnel construction process. By the adoption of the frozen earth waterstop structure, large-scale drainage construction is avoided, precious groundwater resources are saved, and settlement deformation of surrounding adjacent buildings and structures caused by drainage construction is avoided at the same time.