Recently, micro-speakers have attracted much attention due to their increasing demand in mobile devices. Micro-speakers use polymer diaphragms, which are manufactured from thin polymer film by the thermoforming process. The diaphragm is generally designed to be a circular membrane with a cross section consisting of a double dome structure, and a number of corrugations are located in the outer region to produce better sound quality. In the current study, a finite element (FE) analysis is performed for thermoforming, and the resulting thickness reduction in the corrugation regions is estimated. The estimated thickness distribution is used in further structural and modal FE analyses, from which the effects of local thickness reduction on the stiffness and vibration characteristics are determined.