The surface topography characterization of MEMS device is very important to bonding technology of MEMS device. Motif characterizing method is a characterizing method of surface topography by graph. Aiming at the diversity and regionality of surface topography of MEMS device, in this study we have sampled the surface of MEMS device by 3-dimentinal grids using the surface profiler developed by us and characterizes the surface topography of MEMS device by the extended Motif characterizing method. The surface of MEMS device is divided into several Motif regions; the surface topography of every divided region can be evaluated respectively; the details of every region can be zoomed and these regions as a whole or every region can be revolved and projected; one of these regions can be as the reference of other regions. So the height, gradient and other characteristics of others regions of the whole MEMS device surface can be analyzed relative to the reference region; the whole and local surface topography of whole MEMS device can be analyzed.