During insect flight, some overlapping phenomena such as torsion, bending, and warping will appear in the wings, which makes the wings shielded from each other and thus leads to hard discrimination of the flight attitude by traditional optical measurement. To realize the dynamic measurement of mutual occlusion of transparent membranous wings, this paper proposed a three-dimensional (3D) digital image correlation method based on fluorescence polarization imaging to measure the 3D full-field deformation of multi-wing structures. According to the principle of polarization imaging, the 3D morphology of a monochromatic wing can be measured by a single polarization camera in the presence of a splitting optical path integrating mirrors, polarizers and a splitting prism. Depending on the spectral characteristics of fluorescent speckles, different fluorescent speckles were fabricated on different wings that were shielded from each other, and a band-pass filter was used to separate the fluorescent speckles of specific spectra on them, which enabled the independent imaging and synchronous measurement of multiple wings. Firstly, the measurement experiments of the relative surface topography and deformation of the sheet with equal thickness were carried out to calibrate the measurement accuracy of multiple mutually shielded surfaces. Further, the different overlapping forms of insect wings (cicadas) were measured, and the 3D profile of any mutually shielded wings was given to verify the feasibility of the measurement method.