Navel orange is a widely cultivated variety of citrus in southern China. The annual output of citrus has exceeded 60 million tons, indicating the largest producer of citrus with planting area and output ranking first in the world in recent years. However, the damage to navel oranges has been caused by external compression during harvesting and transportation. In this study, an experimental test was conducted on the compression deformation of navel oranges. A systematic analysis was implemented to explore the influence of different compression scales on the damage degree of navel oranges. Some parameters were identified for the damage size of navel oranges. Firstly, the mechanical properties of navel orange were tested by an electronic universal testing machine. The key mechanical parameters of navel orange peel and pulp were measured, such as Young's modulus, yield strength, and Poisson's ratio. The transverse, longitudinal, and oblique compressive strength tests of navel orange were carried out on the load-displacement curves to calculate the ultimate load. The test results showed that the mean compressive limit load of navel orange in the transverse direction was lower than that in the longitudinal and oblique directions under the same deformation. Meanwhile, the navel orange was in the elastic deformation stage, when the compression displacement ranged from 0 to 7.5 mm. Once exceeding this range, the navel orange was in the plastic deformation stage. The damage levels of navel orange were determined under different compression displacements. The compression recovery coefficients of navel orange were obtained to measure the size change of navel orange before and after transverse compression. The microstructure change of the navel orange peel was observed by the paraffin section. At the same time, the navel orange samples after the compression test were stored at room temperature and dark environment. 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 the fruit compression recovery coefficients fluctuated greatly between 10 and 12.5 mm when the compression load was applied to the navel orange. When the compression level was not more than 10 mm, the fruit compression recovery coefficient was close to 0.75. The peel oil cells were intact, indicating almost no damage to the navel orange fruit. Once the compression level reached 12.5 mm, the compression recovery coefficient of the navel orange was significantly reduced, indicating the outstandingly broken peel oil cell. Finally, the three-dimensional solid model of navel orange peel and pulp was constructed by 3D scanner and reverse engineering. The stress distribution of the whole navel orange peel and pulp was also simulated by ANSYS/LS-DYNA. The simulation results showed that the stress of the flesh tissue at a 12.5 mm compression level was very close to the ultimate yield stress. The external load first caused irreversible plastic deformation of the flesh tissue, leading to mechanical damage to the navel orange. The simulation results were consistent with the compression test, which verified the measured mechanical parameters of the navel orange. Therefore, 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 findings can also provide a strong reference for the loss reduction and postharvest storage of navel oranges during harvesting and transportation.