The invention discloses a strongly-permeable stratum deep foundation pit bottom sealing water stopping structure, which comprises diaphragm walls, underwater plain concrete boards, reinforced concrete partition walls, uplift piles and inner supports, wherein the diaphragm walls are arranged around the foundation pit througgh casting; the inner supports support the diaphragm walls; the reinforced concrete partition walls are formed on the foundation pit below the diaphragm walls through casting; the reinforced concrete partition walls and the diaphragm walls of each two faces form a casting block in a surrounding mode on the foundation base; the uplift piles are casted on the foundation base inside the block; each underwater plain concrete board is formed through casting at each block opening formed by the reinforced concrete partition walls and the diaphragm walls in a surrounding mode; and the uplift piles are firmly embedded in the underwater plain concrete boards. The underwater plain concrete boards enhance overall strength and ridigity of the foundation pit bottom, dual effects of reinforced pit bottom and permeation prevention are provided, influences on stability of the pit bottom by high pressure water and raised pit bottom caused by excavation of the foundation pit can be effectively solved, and lateral displacement of the pit wall and settlement deformation of the surrounding enviornment can be well reduced.