Drying significantly influences the quality of micellar casein (MC) powder. This study investigated the effects of three pre-freezing temperatures (−20 °C, −80 °C, and liquid nitrogen) prior to freeze drying on the structure and rennet-induced gelation properties of MC powder. The results showed that as the pretreatment temperature decreased, the degree of disruption to the secondary and tertiary protein structures was reduced, while the particle size gradually increased. In terms of rennet-induced gel properties, the untreated raw MC consistently outperformed all MC powder samples. Among the MC powders, the sample pre-frozen at −80 °C and then freeze-dried (FD-80) exhibited the highest gel strength and a relatively shorter rennet coagulation time. The observed microstructures of the rennet-induced gel were consistent with the rheological results, showing that samples with smaller particle sizes formed more regular and compact gel networks. In conclusion, the MC powder prepared via pre-freezing at −80 °C and then freeze-drying better preserved protein structure and demonstrated superior rennet-induced gel properties, which were closely related to particle size. This study provides theoretical insights for the application of MC powder in products such as cheese, processed cheese, and protein-fortified foods.