This study aimed to explore how storage temperature (25 °C, 4 °C, −20 °C, and −196 °C), drying duration (0, 1, 3, 5 days), and aril removal affect the physiological, biochemical, and microbial community traits of Michelia macclurei seeds. After one month of storage, physiological, biochemical, and microbial indexes were evaluated. Results showed that seeds dried for one day and stored at 4 °C had the highest vigor and germination rates. Storage at 4 °C or −196 °C significantly enhanced antioxidant enzyme activities and affected water content, soluble sugar, protein, malondialdehyde, and amylase levels. Principal component analysis confirmed that retaining arils and drying for 0~1 day before storage at −196 °C or 4 °C was optimal for maintaining seed quality. Microbial analysis revealed that low temperatures increased fungal diversity and bacterial diversity, though bacterial richness decreased compared to 25 °C storage. Ascomycota and Proteobacteria were dominant at the phylum level, while Penicillium and Rhodococcus were the dominant genera. Drying time and aril removal also influenced microbial structure. Overall, moderate drying and low-temperature storage, especially at 4 °C or −196 °C with arils retained, most effectively preserved seed vigor and shaped favorable microbial communities.