Abstract: In order to study the mechanism of response to saline-alkali stress, transcriptome sequencing was performed on Illumina Hiseq^TM on 2 saline-resistant and 1 saline-sensitive 3-year seedlings of Cinnamomun bodinieri. And 6 genes related to arginine and proline pathway were analyzed by qRT-PCR. The results showed that the transcriptional sequencing obtained 72369 Unigenes. Among them, 39156 Unigenes were annotated in NR, NT, KEGG, SwissProt, PFAM, GO and KOG databases.There were 5415 DEGs in the HDHZ vs HJHZ group were founded out and 4003 DEGs were GO annotated, there were 4665 DEGs in the YYHZ vs HJHZ group, of which 331 were GO annotated. KEGG pathway analysis showed that the up-regulated genes in the HDHZ vs HJHZ group were mainly enriched in the pathways related to amino acid metabolism and alkaloid biosynthesis, while the down-regulated genes were mainly enriched in the pathways related to sesquiterpene and triterpene biosynthesis and photosynthesis. The up-regulated genes in YYHZ vs HJHZ group were mainly enriched in sesquiterpene and triterpene biosynthesis and flavonoid biosynthesis pathway. The down-regulated genes were mainly enriched in pigment metabolism and phenolic metabolism-related pathways. Combined with qRT-PCR results of 6 differentially expressed genes, alkaloid, arginine and proline metabolism may play a major role in response to alkali stress, the expression of the obtained genes was consistent with the RNA-Seq data, which confirmed the accuracy of RNA-seq data.