Considering the complex and variability of flight environment of the morphing aircraft, usually it is difficult to solve the real-time wing shape monitoring problem when the aircraft changes its motion state or suffering the wind and waves. In this paper, with the goal of supporting real-time wing shape monitoring of morphing aircraft, three-dimensional (3D) shape monitoring of polyimide film skin for morphing wing based on the embedded Fiber Bragg Grating (FBG) sensor is designed and analyzed. Firstly, the sensitively of FBG sensors with different embedded depth in the polyimide film was analyzed, and the finding is that when the ratio value of upper/lower embedded depth is larger, the sensitively of FBG sensor is higher. Secondly, the wavelength of FBG sensors at different states were obtained, and the center wavelength shift of FBG sensors can be used to measure the bending curvatures of the wing, besides, according to the obtained bending curvatures, the 3D shape of polyimide skin of the morphing wing at different deformation states are reconstructed through interpolation and curve fitting functions. Moreover, several shape reconstruction experiments of the morphing wing were carried out with precise visual measurement, and the maximum error between FBG sensing and visual measurement is 5%. Consequently, the effectiveness of FBG sensing method for wing shape monitoring of morphing aircraft is demonstrated, as well as more potentiality and applicability for the shape monitoring in the field of soft robotics and flexible biosensor monitoring.