Freezing stress (FS), especially during germination, severely impacts the growth, development, productivity, and distribution of alfalfa (Medicago sativa L.). Exogenous salicylic acid (SA), a signal molecule involved in abiotic stress responses, effectively improves the FS response of seeds. We investigate changes in seedling phenotype and hormone contents, and perform transcriptome analyses to identify how SA may improve the FS response in alfalfa during germination. Compared with control values, after 16 h FS, exogenous SA promotes seedling lengthening, and increases endogenous contents of jasmonic, abscisic, and gibberellic acids, and decreases indole-3-acetic acid (IAA), and zeatin; after 24 h FS, contents of SA, IAA, and gibberellic and abscisic acids increased, and JA and zeatin content decreased. Phytohormone biosynthesis and signaling pathways genes were induced by SA after FS. Weighted correlation network analysis suggests that GH3.1 and HSP70 play important roles in SA regulation of FS. We report a possible working model, where exogenous SA inhibits GH3.1 expression to decrease IAA content, causing TIR1 to negatively regulate expression of AUX/IAA and auxin response related genes to suppress the IAA signaling pathway, and for TIR1 to repress the SA signaling pathway after FS. For the NPR1-dependent pathway, NPR1 could bind to TGAs to regulate expression of PR1 genes to defend against FS. For the NPR1-independent pathway, superoxide dismutase, ascorbateperoxidase, glutathione-S-transferase, heat shock protein, alternative oxidase, and late embryogenesis abundant encoded genes were induced following FS.