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In this study, the effects of slow freezing (−20 ℃) and quick freezing (−80 ℃) on the cell wall structure of waxberry fruits were investigated, and the changes of main nutrient quality components during storage were also studied. The moisture content and migration of waxberry fruits during storage were observed by low field NMR. The results showed that the cell wall morphology of quick-frozen waxberry fruits maintained well, and there were obvious gaps in the cross section of the cell wall of slow-frozen waxberry fruits. During the storage period of 25 days, the water content of fruit gradually decreased, but the range of water transfer of quick-frozen waxberry was small, and the total lateral relaxation time was larger than the relaxation time of slow-frozen waxberry, indicating that quick-frozen waxberry could effectively maintain fruit water activity. The free water signal value of quick-frozen waxberry decreased only by 18%, while the free water signal value of slow-frozen waxberry decreased by 47.75%, indicating that quick-frozen waxberry was beneficial to maintaining fruit water content. In addition, fruit nutrients decreased gradually, but the total sugar content, titratable acid content, total phenols and anthocyanins contents were 13.64 mg/g, 13.43 g/L, 15.43 mg/mL and 0.53 μmol/g, respectively, at the end of storage stage of quick-frozen waxberry. The retention rates of main nutritional indexes were higher than those of slow frozen waxberry. Therefore, quick-freezing can effectively delay the loss of nutrients in waxberry fruits.