This paper describes the use of Finite Difference Method (FDM) to analyze a multiple-layered, corrugated rectangular diaphragm subject to residual stress for MEMS applications. The corrugated part of the diaphragm is treated as a flat plate with anisotropic mechanical properties. The multiple-layered structure is treated as a single-layered plate with an effective Young’s modulus. The effect of the residual stresses in the diaphragm layers is simulated with in-plane normal forces in the neutral plane at the four boundary edges of the diaphragm. This way, the complicated analysis on a corrugated, multiple-layered diaphragm with various residual stresses in the layers is greatly simplified, and can be done by FDM without sacrificing accuracy much. Both deflection and stress distribution of the diaphragm under a uniformly applied pressure have been analyzed, although the technique is also applicable for a non-uniform pressure. And we discuss the effects of corrugation depth, period and width on the deflection and stress distribution of the diaphragm. Finally, we describe an example of using this method to design a micromachined, corrugated-diaphragm, piezoelectric microphone in which the residual stress plays a critical role in limiting the performance.