China has become the world's largest producer of citrus with its planting area and output ranking first in the world. In recent years, China's annual output of citrus has exceeded 60 million tons. Navel orange is the main variety of citrus and is widely cultivated in southern China. In view of the damage of navel oranges caused by external compression during harvesting and transportation, this paper conducted an experimental study on the compression deformation process of navel oranges, analyzed the influence of different compression scales on the damage degree of navel oranges, and explored the parameter identification method of the damage size of navel oranges. Firstly, the mechanical properties of navel orange were tested by electronic universal testing machine. And the key mechanical parameters of navel orange peel and pulp such as Young's modulus, yield strength and Poisson's ratio were measured respectively. Through the transverse, longitudinal and oblique compressive strength tests of navel orange, the load-displacement curves in the above three directions were obtained, and the ultimate load was calculated. The test results showed that the mean compressive limit load of navel orange in transverse direction is lower than that in longitudinal and oblique direction under the same deformation conditions. Meanwhile, the navel orange is in the elastic deformation stage when the compression displacement ranges from 0 to 7.5mm, while it is in the plastic deformation stage when it exceeds the range. On this basis, the damage law of navel orange under different compression displacement conditions was studied. The compression recovery coefficient of navel orange was obtained by measuring the size change of navel orange before and after transverse compression. And the microstructure change of navel orange peel was observed by paraffin section. At the same time, the navel orange samples after compression test were stored under room temperature and dark environment, and the mass loss rate was measured regularly to evaluate the damage degree of navel orange under different compression conditions from macro and micro perspectives. The results showed that when the compression load was applied to navel orange, the fruit compression recovery coefficient fluctuated greatly between 10 mm and 12.5 mm. When the compression level was not more than 10 mm, the fruit compression recovery coefficient was close to 0.75, and the peel oil cells were intact, which means there was almost no damage to navel orange fruit. When the compression level reached 12.5 mm, the compression recovery coefficient of navel orange was significantly reduced, and the peel oil cell was obviously broken. Finally, the three-dimensional solid model of navel orange peel and pulp was constructed by 3D scanner and reverse engineering, and the stress distribution of the whole navel orange peel and pulp was analyzed by ANSYS/LS-DYNA. The simulation results showed that the stress of the flesh tissue at 12.5mm compression level was very close to the ultimate yield stress, and the external load first caused irreversible plastic deformation of the flesh tissue, making it more likely to cause mechanical damage to the navel orange. The simulation results were consistent with the results of the compression test, which verified the correctness of the measured mechanical parameters of the navel orange. It can be seen that the extrusion deformation range of navel orange should be controlled within 10 mm and the external load should not exceed 63.24 N in the process of low-loss harvesting and transportation. The results can provide reference for loss reduction design and postharvest storage of navel orange during harvesting and transportation.