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In the handling or processing process, fruits are easily crushed by external loads. This type of damage in fruit often leads to the internal pulp browning and rotting, with the severity largely dependent on the fruit tissue’s geometric and mechanical properties. In kiwifruits, with their thin skin and dark-colored flesh, it is particularly challenging to observe and analyze the damage caused by extrusion through traditional experimental methods. The objective of this research is to construct a multi-scale finite element model encompassing the skin, flesh, and core by measuring the geometric and mechanical properties of kiwifruit, to assess and predict the damage characteristics under compression, and to verify the accuracy of the finite element model through experiments. The results indicated that kiwifruits demonstrated different compressive strengths in different directions during compression. The compressive strength in the axial direction was higher than that in the radial direction, and there was little difference between the long and short radial directions. The flesh tissue is the most vulnerable to mechanical damage under external compression, followed by the core. At strain levels below 5%, there was no noticeable damage in the axial or radial directions of the kiwifruit. However, when strain exceeded 5%, damage began to manifest in some of the flesh tissue. To maintain fruit quality during storage and transportation, the stacking height should not exceed 77 fruits in the axial direction, 48 in the long direction, and 53 in the short direction. The finite element analysis showed that the established model can effectively simulate and predict the internal damage behavior of kiwifruits under compression loads, which is helpful for a deeper understanding of the mechanical properties of fruits and provides a theoretical basis and technical guidance for minimizing mechanical damage during fruit handling.