Three-dimensional chiral materials with intrinsic chirality play a crucial role in achieving a strong chiral response and flexible light manipulation. Reconfigurable chirality through the 3D morphological transformation of chiral materials is significant for greater freedom in tailoring light but remains a challenge. Inspired by the unique 3D morphological memory capability of shape memory alloys (SMAs), we demonstrate and discuss a chiral resonator in the microwave regime that can realize reconfigurable chirality through 3D morphological transformation. The introduction of heating film realizes voltage control of SMA’s morphology for utilizing the temperature sensitivity of SMA better, enabling arbitrary control of circular dichroism (CD) flip and CD intensity. The qualitative and quantitative analysis of the surface current distribution of chiral enantiomers reveals that the chirality of meta-atoms originates from the surge of electric dipole px and electric quadrupole Q. It is worth mentioning that the proposed strategy to achieve reconfigurable chirality using 3D morphological transformations can be directly extended to other higher frequencies, such as visible, infrared, and terahertz bands. Significantly, our paradigm to study the relationship between complex 3D morphology and chirality holds potential for application in biosensing, spin detection, and spin-selective devices.