The accurate determination of residual stress/strain in thin films is especially important in the emerging field of MicroElectroMechanical Systems (MEMS). In this article, a focused ion beam (FIB) moiré method is proposed and demonstrated to measure the strain in MEMS structures. This technique is based on the advantages of the FIB system in nano-fabrication, imaging, in-situ deposition, and fine adjustment. Nano-grating lines with 70 nm width and 140 nm spacing are directly written on the top of the MEMS structures by ion milling without the requirement of an etch mask. The FIB moiré pattern is formed by the interference between a prepared specimen grating and FIB raster scan lines. The strain of the MEMS structures is derived by calculating the average spacing of moiré fringes. Since the local strain of a MEMS structure itself can be monitored during the process, the FIB moiré technique has many potential applications in the mechanical metrology of MEMS. As an example, the strain distribution along the sticking MEMS structures, and the contribution of surface oxidization and mass loading to the cantilever strain is determined by this FIB moiré technique.