Constant-frequency ultrasonic treatment helped to improve seed germination. However, variable-frequency ultrasonic treatment on maize seed germination were rarely reported. In this study, maize seeds were exposed to 20–40 kHz ultrasonic for 40 s. The germination percentage and radicle length of maize seeds increased by 10.4% and 230.5%. Ultrasonic treatment also significantly increased the acid protease, α-amylase, and β-amylase contents by 96.4%, 73.8%, and 49.1%, respectively. Transcriptome analysis showed that 11,475 differentially expressed genes (DEGs) were found in the ultrasonic treatment and control groups, including 5,695 upregulated and 5,780 downregulated. Metabolic pathways and transcription factors (TFs) were significantly enriched among DEGs after ultrasonic treatment. This included metabolism and genetic information processing, that is, ribosome, proteasome, and pyruvate metabolism, sesquiterpenoid, triterpenoid, and phenylpropanoid biosynthesis, and oxidative phosphorylation, as well as transcription factors in the NAC, MYB, bHLH, WRKY, AP2, bZIP, and ARF families. Variable-frequency ultrasonic treatment increased auxin, gibberellin, and salicylic acid by 5.5%, 37.3%, and 28.9%, respectively. Abscisic acid significantly decreased by 33.2%. The related DEGs were upregulated and downregulated to varying degrees. Seed germination under the abiotic stress conditions of salt stress (NaCl solution), drought (PEG solution), and waterlogging (water-saturated sand bed) under ultrasonic treatment were promoted, radicle length was significantly increased by 30.2%, 30.5%, and 27.3%, respectively; and germination percentage by 14.8%, 20.1%, and 21.6%, respectively. These findings provide new insight into the mechanisms through ultrasonic to promote maize seed germination.