The invention discloses a Y-TOOL by-pass stopper. The Y-TOOL by-pass stopper comprises a conical cup, an inserted positioning seal, a screwed joint, a skeleton short piece, a connecting swivel nut, alengthened short piece and an O-type seal ring. The screwed joint is in threaded connection with one end of the skeleton short piece, the other end of the skeleton short piece is in threaded connection with one end of the lengthened short piece through the connecting swivel nut, the other end of the inserted positioning seal is inserted into a working barrel connected with one port of a Y-TOOL, the conical cup is arranged on the skeleton short piece, located in an oil pipe connected with the other port of the Y-TOOL, and used for sealing the annulus between the skeleton short piece and the oilpipe, the skeleton short piece, the lengthened short piece and the inserted positioning seal are of tubular structures, and a killing well channel is formed in the skeleton short piece, the lengthened short piece and the inserted positioning seal. With the Y-TOOL by-pass stopper, safety risks can be reduced, and operating cost can be lowered.