Seed germination is a crucial developmental event in the plant life cycle. Proper germination significantly impacts the yield and quality. This study focuses on macadamia nuts, exploring the physiological, metabolic, and molecular biological characteristics during seed germination. The water content of macadamia seeds reached a peak in the seed imbibition stage, followed by a gradual decline. Key components such as fats, proteins, and soluble sugars decreased consistently. The enzyme activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and glutathione peroxidase (GPX) increased throughout seed germination, reaching peak levels in leaf growth stages. A total of 1523 metabolites and 13,035 differentially expressed genes (DEGs) were detected by transcriptomic and metabolomic analyses, among which 1320 were transcription factors. The transcriptome and metabolome integration analysis showed significant overlaps between DEGs and differential metabolites in pathways such as phenylpropanoid biosynthesis. Quercetin, trifolin, rutin, myricetin, and quercetin 3-beta-D-sophoroside may play important roles in seed germination. FG2 and CYP75A/CYP75B1 were key genes in the flavonoid pathway. Hormones such as auxin (IAA), cytokinin (CTK), gibberellin (GA), and abscisic acid (ABA) exhibited stage-specific changes during germination. This study provided important theoretical basis and practical guidance for optimizing seed germination rates and enhancing stress resistance capabilities.