Soil salinization is one of the main problems leading to a reduction in arable land area. In the present study, strongly salt-tolerant lines were screened for germination rates and physiological indices. The mechanism of saline-alkali stress tolerance in winter rapeseed was examined using transcriptome and metabolome analyses. The saline-alkali tolerant variety (SCKY-6-27) had higher SOD, POD, CAT, and soluble protein levels than the saline-alkali-sensitive variety, whereas the saline-alkali-tolerant variety showed lower MDA levels. Winter rapeseed responded to saline-alkali stress mainly by engaging in phytopathogen interactions, regulating starch and sucrose metabolism, activating the MAPK signaling pathway, and utilizing other pathways. Furthermore, WGCNA analysis showed that seven main pathways were involved, the most significant of which was the plant hormone signaling pathway. Combined analysis of the transcriptome and metabolome showed that the most significant pathways with regard to the enrichment of differentially expressed genes and differential metabolites under high saline-alkali stress conditions were starch, sucrose metabolism, and plant hormone signaling. Through comprehensive screening and analysis of rapeseed genes and metabolites under saline-alkali stress, changes in molecular mechanisms and metabolic pathways in rapeseed responding to saline-alkali stress were revealed, providing a new direction for the in-depth exploration of saline-alkali resistance mechanisms of rapeseed.