Sucrose (300 mM) is a lyoprotectant for CPX-351 (cytarabine/daunorubicin co-loaded liposome). However, its high hygroscopicity leads to crystallization, limiting long-term storage stability. Considering this, we investigated alternative options, such as trehalose, raffinose, and mannitol, known for their lower hygroscopicity or crystallinity than sucrose. Consequently, lyophilized liposomes co-loaded with cytarabine and daunorubicin using sucrose, trehalose, a sucrose-raffinose combination, mannitol, and glucose were created and investigated, respectively. The results, which include particle size changes and drug retention rates, suggest that sucrose, trehalose, and the sucrose-raffinose combination (mass ratio 7:3) exhibit superior and similar freeze-drying protective effects. FTIR, PXRD, and DSC analyses were employed to understand the protective mechanisms and capabilities of these lyoprotectants. FTIR and PXRD results revealed the presence of hydrogen bond interactions between the lyoprotectants and phospholipids, and the interaction strength order was trehalose ≈ sucrose-raffinose combination (mass ratio 7:3) > sucrose > glucose > mannitol, with their vitrification ability corresponding to this order. DSC determinations indicated that sucrose-raffinose combination (mass ratio 7:3), sucrose, and trehalose were better at inhibiting the T_m (temperature of gel-to-liquid crystalline phase transition during dehydration) compared to glucose and mannitol. In summary, the protective capability of lyoprotectants is closely tied to their vitrification ability and their hydrogen bond interaction with phospholipids, thus preventing aggregation/fusion and reducing the T_m of liposomes during lyophilization. The sucrose-raffinose (mass ratio 7:3) combination and trehalose, with their superior lyophilization protective capability and lower hygroscopicity, offer promising replacements for sucrose in co-loaded liposome lyophilization.