The waxy composition of blueberry epidermis seriously hinders the diffusion of water during its vacuum freeze-drying (VFD) process. Fresh blueberries were used as raw materials to investigate the effects of three ultrasonic methods on the wax layer and cell structure of blueberries. Combining the crisp quality and drying characteristics of blueberries, the suitable ultrasonic pretreatment methods for vacuum freeze-drying of blueberries was explored in the study. The results of gas chromatography-mass spectrometry analysis showed that three ultrasonic treatments had different effects on the wax composition and content of blueberry epidermis. The wax composition and total relative content of intermittent ultrasonic treatment showed the greatest changes, with a 35% decrease in total relative content compared to the control group. The results of microstructure analysis indicated that, after probe and intermittent ultrasonic treatment, the wax distribution on the blueberry epidermis was loose, and the skin was exposed. After continuous ultrasonic treatment, the wax crystal structure of blueberry epidermis changed from tubular to flaky. Probe and intermittent ultrasonic treatment had significant damage to the internal cellular structure of blueberries, forming large-sized micro-channels. Moreover, after probe ultrasonic treatment, the cell membrane permeability of blueberries was significantly higher than that of other treatment methods (P<0.05). After different ultrasonic treatments, the T₂ relaxation spectra of blueberries shifted to the left as a whole, and the peak area and signal amplitude decreased. Three ultrasonic treatment methods significantly improved the drying rate of VFD blueberries, and the continuous and probe ultrasonic treatment significantly improved the brittleness of VFD blueberries, increasing by 40.12% and 38.27%, respectively. After the continuous ultrasonic pretreatment, the retention rates of vitamin C and anthocyanins in VFD blueberries were significantly increased, reaching 86.17%±0.18% and 71.30%±1.88%, respectively. By comprehensive comparison, the continuous ultrasonic treatment was an optimal pre-treatment for VFD blueberries.