Honeycomb structures have attracted much attention in various engineering fields due to its superiorities in high specific strength, high specific stiffness and excellent energy-absorbing characteristics. Therefore, it is very important to obtain the deformation state of honeycomb structure in the studies of its manufacturing process and mechanical behavior. In this study, a simple and efficient strategy for tracking the deformation of thin-walled honeycomb structure based on image skeletonization and branch points matching is presented. Principle and process of the new proposed strategy are first detailed, including image skeletonization, branch points selection, matching expansion and deformation calculation, etc. Simulations and experiments with compression and tensile deformations are performed to verify the efficiency of the proposed strategy. The results indicate that the displacement measurements based on the proposed strategy are able to provide subpixel-level accuracy, even though some interference branch points are generated during deformation. In addition, the limitations of the proposed strategy are discussed, which points out the train of thought for the subsequent research.