Abstract: 【Objective】 This study aimed to investigate the secondary metabolism-related pathways involved in flower bud differentiation of mango，so as to provide reference for elucidating the molecular mechanism of mango flower bud differentiation and ensuring the stable and high yield for mango industry.【Method】 Guifei mango was used as the experimental material for flower removal treatment，and axillary bud samples were collected at three time points. The treated samples were labeled as T1，T2，and T3，and the control samples as CK1，CK2，and CK3. Transcriptome sequencing was performed on different samples using next-generation sequencing technology. Differentially expressed genes （DEGs） of the three comparison groups （CK1 vs T1，CK2 vs T2，and CK3 vs T3） were screened with the criteria of log₂ Fold Change > 1 and P < 0.05，followed by GO functional annotation and KEGG signaling pathway enrichment analysis of DEGs. Metabolites in the samples were detected and analyzed by liquid chromatography-mass spectrometry（LC-MS），and differentially accumulated metabolites （DAMs） of the three comparison groups were screened with the criteria of variable importance projection （VIP） > 1 and P < 0.05. Combined transcriptome and metabolome analysis were conducted on plant hormone signal transduction and phenylalanine metabolism pathways，and the transcriptome sequencing data of four DEGs were verified by real-time fluorescence quantitative PCR （qRT-PCR）.【Result】 Transcriptome sequencing revealed that a total of 8796 DEGs were detected in the 3 comparison groups. The numbers of up-regulated DEGs in CK1 vs T1，CK2 vs T2， and CK3 vs T3 were 2215，3013，and 3316 respectively，and the numbers of down-regulated DEGs were 1419，2146，and 2747 respectively. GO functional annotation showed that the three comparison groups were all annotated to cell cycle in the biological process category，annotated to supramolecular polymer and supramolecular fiber in the cellular component category，and annotated to microtubule motor activity in the molecular function category. KEGG signaling pathway enrichment analysis indicated that the shared significantly enriched pathways in the three comparison groups included flavonoid biosynthesis，phenylalanine，tyrosine and tryptophan biosynthesis，starch and sucrose metabolism. Metabolome sequencing analysis showed that the numbers of content up-regulated DAMs in CK1 vs T1，CK2 vs T2，and CK3 vs T3 comparison groups were 41，33，and 53 respectively，and the numbers of content down-regulated DAMs were 20，41，and 55 respectively. KEGG metabolic pathway enrichment results revealed that the shared significantly enriched metatolic pathways of the three comparison groups were flavonoid biosynthesis，phenylalanine metabolism，starch and sucrose metabolism. Combined analysis demonstrated that there were three plant hormones with increased contents， which were auxin （IAA）， abscisic acid （ABA）， and jasmonic acid （JA），and there were two plant hormones with clecerased conrents， which were cytokinin （CTK） and gibberellin （GA）. After flower removal in mango，seven genes were involved in the IAA signaling transduction pathway，among which two genes were up-regulated. In the CTK signaling transduction pathway，type-B Arabidopsis response regulator （B-ARR） gene family contained both up- and down-regulated genes. In GA signaling transduction，Some members of GID1 and DELLA family genes were down-regulated. A total of 26 DEGs and 9 DAMs involved in the phenylalanine metabolism pathway were jointly identified by transcriptome and metabolome analysis，including PAL，AST，and TAT genes. qRT-PCR results showed that the relative expression levels of the four genes involved in phenylalanine metabolism were consistent with the FPKM values from transcriptome sequencing.【Conclusion】 Plant hormone signaling transduction and phenylalanine metabolism are important secondary metabolic pathways affecting mango flower bud differentiation. After flower removal，these two pathways influence the coordinated regulation of carbohydrate metabolism，nitrogen metabolism，and tyrosine metabolism by altering hormone composition，differential gene expression，and generating secondary DAMs，thereby affecting mango flower bud differentiation.