Aluminum-based adjuvants have been indispensable to vaccine potency. However, their effectiveness is difficult to maintain after freeze-drying, which limits the storage and application of aluminum-adjuvanted vaccines. In this study, the impact of freeze-drying on aluminum oxyhydroxide nanorods (AlOOH NRs) was investigated. Freeze-drying led to aggregation and resulted in the loss of the surface hydroxyl content of aluminum adjuvants. To alleviate freeze-drying-induced damage, the potency of different alkyl glycosides as protectants was further evaluated. It was demonstrated that the structural balance of the head and tail of a glycoside was more conducive to protecting AlOOH NRs from aggregation and loss of surface hydroxyl groups. These results underline the proper selection of protectants to protect adjuvants against functional defects caused by freeze-drying, which is important for the stability and efficacy of vaccines and biopharmaceutical products.