To provide a manufacturing method of a cap with a liner, and a cap with a liner and a bottle with a cap having excellent plug-openability, sealability, sanitary property, recyclability and molding workability or the like.

In the manufacturing method, the cap 1 with the liner capable of closing a mouth piece part of a bottle is manufactured by installing the liner 5 in a cap shell 4 comprising a top plate part 2 and a cylindrical circumferential wall part 3 hanging from a circumferential edge of the top plate part 2. The manufacturing method comprises a hard sheet installing step of inserting a disk-shaped hard sheet 5a in the cap shell 4 while being brought into contact with an inner surface of the top plate part 2, and a flexible layer forming step of forming a flexible layer 5b more flexible than the hard sheet 5a by the resin molding on the hard sheet 5a in an inserted state.