There is provided a method for filling a multilayer bottle including outermost and innermost layers and at least one barrier layer interposed between the outermost and innermost layers, with a material to be stored therein. In the filling method, the material to be stored is filled in the multilayer bottle having the barrier layer satisfying a specific glass transition point (Tg) and a specific water content as measured by a Carl-Fisher method at 230° C. for 30 min. The multilayer bottle obtained by the filling method of the present invention hardly undergoes delamination between the layers owing to dropping or impact, and is applicable to a filling method such as hot filling.