[Objective] Bombax ceiba is an important ornamental plant in Southern China. The study on the difference in gene expression of B. ceiba 's dark-red-line and yellow-line at different stage, analyzing the relationship between gene expression and flower color, would provide scientific basis for revealing the mechanism of B. ceiba color variation and establishing a B. ceiba color-oriented breeding technology system. [Method] Taking the dark-red-line and yellow-line of B. ceiba flower as materials, the petal tissues of the two flower colors at different development stages were collected, and the Illumina HiSeqTM 4000 was used for transcriptome sequencing. DESeq2 was used for differentially expressed genes (DEGs) analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) database was used for pathway enrichment analysis. [Results] A total of 75,190 unique genes were obtained by sequencing, and 4,772 single genes were annotated by at least one of the public databases of Nr, SwissSProt, COG and KEGG. The results of KOG functional enrichment analysis showed that the genes were enriched in general function prediction, signal transduction mechanisms, and posttranslational modification, protein turnover, chaperones. A total of 10,397 DEGs were obtained and significantly enriched in 29 biological pathways, among which the most significantly enriched pathway was photosynthesis, followed by metabolic pathways and plant hormone signal transduction. A total of 72 DEGs involved in the phenylpropanoid biosynthesis, 25 DEGs involved in the carotenoid biosynthesis, the flavonoid biosynthesis, the phenylalanine metabolism respectively were identified. These pathways and genes were all related to the biosynthesis of anthocyanins. Another 4 DEGs were significantly enriched in betalain biosynthesis. The results of qRT-PCR transcriptome data was reliable. [Conclusion] The genes related to photosynthesis, metabolic pathways, plant hormone signal transduction pathways, flavonoid biosynthesis pathways, phenylpropane biosynthesis pathways and energy metabolism pathways are involved in the development of different flower colors at different stages. The important synthase genes of flavonoid biosynthesis pathway are highly expressed in the middle stage and bloom stage of dark-red line, which may be the main reason for the dark-red flower color. Some family members of the key synthase genes of the carotenoid biosynthesis pathway are highly expressed during the bud and mid-bud stage of yellow-flower line, which may be the main reason for the yellow flower color.