Flexible chiral honeycomb cores generally exhibit nonlinear elastic properties due to large geometric deformation. The effective elastic moduli and Poisson’s ratio typically vary with an increase in deformation. Here, the size and shape optimization of the chiral hexagonal honey-combs was performed to keep the Young’s moduli and Poisson’s ratio unchanged under large deformations. The size of the honeycomb unit cell and the position coordinates of the key points were defined simultaneously as design variables. The equivalent Young’s modulus and Poisson’s ratio of chiral honeycombs were calculated through geometric nonlinear analysis. The objective was to minimize the allowable tolerance between the prescribed and actual properties within the range of the target strain. A genetic algorithm was then adopted. The optimal results demonstrate that the chiral honeycombs can maintain effective elastic properties that do not vary under large deformation. These results are meaningful to morphing aircraft designs.