The invention relates to a water stop structure between a steel cofferdam side wall and base sealing concrete and a construction method thereof. The water stop structure comprises a steel cofferdam side wall and base sealing concrete, wherein the base sealing concrete is poured on the bottom of the steel cofferdam side wall; the side embedded into the base sealing concrete of the steel cofferdam side wall is fixedly connected with a water stop steel plate; the water stop steel plate is embedded into the base sealing concrete; a grouting perforated pipe is arranged on the water stop steel plate; a plurality of through holes are formed in the outer wall of the grouting perforated pipe at intervals; the outside of the grouting perforated pipe is sleeved with a film. The water stop structure has the advantages that multiple water stop barriers are arranged, the water seepage situation generated in later construction can be effectively prevented, and the water-free operation environment inthe cofferdam can be ensured.