The morphing aircraft can adaptively change the aerodynamic layout according to the mission requirements to obtain the optimal flight quality. The flexible skin composed of flexible skin and honeycomb support structure is one of the key structural forms to realize the configuration change of morphing aircraft. However, due to the influence of Poisson effect, the flexible skin is prone to produce out-of-plane deformation modes such as "dent" and "bump" during deformation. Therefore, the effects of elastic modulus, Poisson's ratio, skin thickness, cell size and honeycomb configuration on out-of-plane deformation were studied. Then, based on the hole filling method, the deformation characteristics of the filler and the honeycomb wall under well bonded and unbonded conditions were analyzed. The results show that the out-of-plane deformation of the flexible skin and the related parameters do not all show a linear relationship. Filling elastic material in the honeycomb cell can inhibit the out-of-plane deformation of the flexible skin, but whether the filling material is well bonded to the honeycomb wall has a great influence on the out-of-plane deformation of the flexible skin, which needs to be paid attention to in engineering design.