To improve the performance of variable area wing and realize smooth and flexible deformation, a new variable area wing design based on negative Poisson’s ratio honeycomb structure is proposed. Firstly, the negative Poisson’s ratio honeycomb structure element is applied to the design of variable area wing. By using the auxetic characteristics of the negative Poisson’s ratio element, the wing structure undergoes both span direction and chord direction deformation, so as to achieve greater area change. Then, in order to realize the deformation control of variable area wing structure, a new type of honeycomb structure unit with local negative Poisson’s ratio adjustable is designed. The control rules for its relative elastic modulus and Poisson’s ratio are analyzed by finite element simulation. Finally, by optimizing the parameters of the honeycomb structure unit in the wing structure, the deformation control ability of honeycomb structure unit is validated. The results show that when the deformation of the wing structure along the span direction is 10.0%, the variable-area wing achieves a 23.9% area change. Furthermore, the deformed contour of the wing structure matches the target contour well, with a shape error of only 1.09%. The wing structure also exhibits good bearing performance. For a variable area wing structure made of 7075 aluminum alloy, the maximum out-of plane-displacement is 0.645 mm under the aerodynamic load of 15 kPa. The feasibility of variable area wing design based on negative Poisson’s ratio honeycomb structure is preliminarily validated, which provides a new idea for the design of variable area wing structures.