Salinity stress is a major abiotic factor that adversely affects plant growth and development. This study investigated the physiological and molecular responses of Brassica rapa L. ssp. Pekinensis to salinity stress by subjecting seedlings to varying concentrations of NaCl. Physiological analysis revealed significant wilting, chlorosis, and a marked reduction in chlorophyll and carotenoid contents in NaCl-treated seedlings, indicating impaired photosynthetic efficiency and oxidative stress mitigation. RNA-seq analysis identified extensive transcriptional reprogramming, with 6693 and 10,280 differentially expressed genes (DEGs) in Z150 and Z300 treatments, respectively, compared to the control group. DEGs were clustered into six expression trends, with sustained up-regulation in Clusters 2 and 6 and down-regulation in Cluster 3. Gene Ontology (GO) enrichment analysis highlighted the involvement of these DEGs in stress responses. Key DEGs encoding heat shock proteins, peroxidases, glutathione S-transferases, and transcription factors were significantly induced under salinity stress, suggesting their roles in stress adaptation. Furthermore, GO and KEGG enrichment analyses revealed significant down-regulation of genes associated with photosynthesis and carbon metabolism, indicating disruption of these critical pathways. Weighted Gene Co-expression Network Analysis (WGCNA) identified hub genes, such as histidine synthase and low-density receptor-like protein, potentially central to salinity stress responses. Additionally, carotenoid metabolism was significantly inhibited, with down-regulation of key genes in the carotenoid biosynthesis pathway. RT-qPCR validation confirmed the reliability of the RNA-seq data. Collectively, these findings provide comprehensive insights into the physiological and molecular mechanisms underlying response of B. rapa L. ssp. Pekinensis to salinity stress, highlighting potential targets for improving salinity tolerance in crops.