In a method for manufacturing a thermoplastic resin vessel, in which a cup-shaped vessel is thermally formed from a thermoplastic resin sheet by a plug, the method including the steps of: pre-forming a portion of the thermoplastic resin sheet corresponding to an orifice portion or a flange portion of the cup-shaped vessel; and clamping the pre-formed portion of the thermoplastic resin sheet to accomplish the forming. According to the manufacturing method, thickening of a vessel bottom part and warpage of the flange portion can be improved.