A thermal deformation measurement system based on calibrated phase-shifting digital holography is proposed. Two synchronized ordinary CMOS cameras are used in the calibrated phase-shifting digital holography system. One is to record the holograms including the object information, and the other is to record the interference fringes to evaluate phase-shifting errors. The calibrated phase-shifting digital holography can provide the high quality reconstructed images which are applied to calculate the thermal deformation of the object. Meanwhile, the thermal images of the object at different temperatures are recorded by a thermal camera. Nanometer-order thermal deformation measurement of an electronic device is achieved in a real experiment. Our measurement system could be useful for electric packaging materials development or the system design.