This invention relates to a method of making a multilayer container which comprises: a primary stretching and heat-setting process wherein a multilayer sheet comprising a A-PET layer, a functional resin layer and a sealant layer, is heated, primarily stretched and then primarily heat-set, and a secondary stretching and heat-setting process wherein the multilayer sheet treated in the primary stretching and heat-setting process is molded with heating by a mold of a thermoforming machine while secondary stretching is performed, followed by secondary heat-setting in the same mold.